# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'prodigal'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/prodigal'
require 'pp'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
require 'pp'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
casts = []
casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
class Velvet
def initialize(directory, sequence_file, verbose)
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
require 'pp'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/seq'
casts = []
casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
def disambiguate(adaptor)
adaptor_disamb = adaptor.dup
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'prodigal'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/prodigal'
casts = []
casts << {:long=>'full', :short=>'f', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
require 'pp'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
require 'pp'
MID_LEN = 10
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/seq'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
require 'pp'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
ILLUMINA_BASE = 64
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/seq'
require 'pp'
class Pcr
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
require 'gnuplot'
require 'pp'
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
casts << {:long=>'no_stream', :short => 'x', :type => 'flag', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fastq'
+require 'maasha/biopieces'
+require 'maasha/fastq'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'genbank'
+require 'maasha/biopieces'
+require 'maasha/genbank'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'sff'
+require 'maasha/biopieces'
+require 'maasha/sff'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
require 'pp'
MID_LEN = 10
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
ILLUMINA_BASE = 64
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'seq'
+require 'maasha/biopieces'
+require 'maasha/seq'
require 'pp'
class Seq
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
+require 'maasha/biopieces'
casts = []
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
+require 'maasha/biopieces'
+require 'maasha/fasta'
class Uclust
include Enumerable
### Here we add the Biopieces Ruby libraries to RUBYLIB.
-export RUBYLIB="$RUBYLIB:$BP_RUBY/Maasha/lib"
+export RUBYLIB="$RUBYLIB:$BP_RUBY/lib"
### Some useful aliases.
+++ /dev/null
-require 'rake/testtask'
-
-Rake::TestTask.new("test") do |t|
- t.pattern = "test/test_*.rb"
- t.warning = true
-end
+++ /dev/null
-# Copyright (C) 2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Error class for all exceptions to do with Base36.
-class Base36Error < StandardError; end
-
-ALPH = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
-BASE36 = 36
-
-# Class containing methods to encode and decode Base 36.
-# Note that the ALPH is [alph + num] and not [num + alph]
-# which prevents us from simply using .to_i(36) and .to_s(36).
-#
-# http://en.wikipedia.org/wiki/Base_36
-class Base36
- # Method that encodes an integer into a base36 string
- # that is returned.
- def self.encode(num)
- raise Base36Error unless num.is_a? Fixnum
-
- base36 = ""
-
- while num > 0
- base36 << ALPH[(num % BASE36)]
- num /= BASE36
- end
-
- base36 << ALPH[0] if num == 0
-
- base36.reverse
- end
-
- # Method that decodes a base36 string and returns an integer.
- def self.decode(base36)
- raise Base36Error if base36.empty?
-
- result = 0
- pos = 0
-
- base36.upcase.reverse.each_char do |char|
- result += ALPH.index(char) * (BASE36 ** pos)
- pos += 1
- end
-
- return result;
- end
-end
-
-__END__
+++ /dev/null
-raise "Ruby 1.9 or later required" if RUBY_VERSION < "1.9"
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'fileutils'
-require 'date'
-require 'optparse'
-require 'open3'
-require 'pp'
-
-# Biopieces are command line scripts and uses OptionParser to parse command line
-# options according to a list of casts. Each cast prescribes the long and short
-# name of the option, the type, if it is mandatory, the default value, and allowed
-# and disallowed values. An optional list of extra casts can be supplied, and the
-# integrity of the casts are checked. Following the command line parsing, the
-# options are checked according to the casts. Methods are also included for handling
-# the parsing and emitting of Biopiece records, which are ASCII text records consisting
-# of lines with a key/value pair separated by a colon and a white space ': '.
-# Each record is separated by a line with three dashes '---'.
-class Biopieces
- include Enumerable
-
- attr_accessor :out # accessor for out stream _ios_
-
- # Initialize a Biopiece and write the status to file.
- # Options are for testing purposes only.
- def initialize(test=nil, input=STDIN, output=STDOUT)
- @test = test
- @input = input
- @output = output
- end
-
- # Check the integrity of a list of casts, followed by parsion options from argv
- # and finally checking the options according to the casts. Returns nil if argv
- # is empty, otherwise an options hash.
- def parse(argv, cast_list=[], script_path=$0)
- casts = Casts.new(cast_list)
- option_handler = OptionHandler.new(argv, casts, script_path, @test)
- @options = option_handler.options_parse
- end
-
- # Open Biopiece input stream if not open and iterate over all Biopiece
- # records in the stream.
- def each_record
- @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
- return if @in.nil?
-
- record = {}
-
- @in.each_line do |line|
- case line
- when /^([^:]+): (.*)$/
- record[$1.to_sym] = $2
- when /^---$/
- yield record unless record.empty?
- record = {}
- else
- raise "Bad record format: #{line}"
- end
- end
-
- yield record unless record.empty?
-
- self # conventionally
- end
-
- alias :each :each_record
-
- # Open Biopiece output stream if not open and puts record to the stream.
- def puts(record)
- @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
-
- record.each do |key,value|
- @out.print "#{key.to_s}: #{value}\n"
- end
-
- @out.print "---\n"
- end
-
- def to_s
- end
-
- # Create a temporary directory inside the ENV["BP_TMP"] dir.
- def mktmpdir
- time = Time.now.to_i
- user = ENV["USER"]
- pid = $$
- path = ENV["BP_TMP"] + "/" + [user, time + pid, pid, "bp_tmp"].join("_")
- Dir.mkdir(path)
- Status.new.set_tmpdir(path)
- path
- end
-end
-
-
-# Error class for all exceptions to do with option casts.
-class CastError < StandardError; end
-
-
-# Class to handle casts of command line options. Each cast prescribes the long and
-# short name of the option, the type, if it is mandatory, the default value, and
-# allowed and disallowed values. An optional list of extra casts can be supplied,
-# and the integrity of the casts are checked.
-class Casts < Array
- TYPES = %w[flag string list int uint float file file! files files! dir dir! genome]
- MANDATORY = %w[long short type mandatory default allowed disallowed]
-
- # Initialize cast object with an optional options cast list to which
- # ubiquitous casts are added after which all casts are checked.
- def initialize(cast_list=[])
- @cast_list = cast_list
- ubiquitous
- check
- long_to_sym
- self.push(*@cast_list)
- end
-
- private
-
- # Add ubiquitous options casts.
- def ubiquitous
- @cast_list << {:long=>'help', :short=>'?', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- @cast_list << {:long=>'stream_in', :short=>'I', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- @cast_list << {:long=>'stream_out', :short=>'O', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- @cast_list << {:long=>'verbose', :short=>'v', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- end
-
- # Check integrity of the casts.
- def check
- check_keys
- check_values
- check_duplicates
- end
-
- # Check if all mandatory keys are present in casts and raise if not.
- def check_keys
- @cast_list.each do |cast|
- MANDATORY.each do |mandatory|
- raise CastError, "Missing symbol in cast: '#{mandatory.to_sym}'" unless cast.has_key? mandatory.to_sym
- end
- end
- end
-
- # Check if all values in casts are valid.
- def check_values
- @cast_list.each do |cast|
- check_val_long(cast)
- check_val_short(cast)
- check_val_type(cast)
- check_val_mandatory(cast)
- check_val_default(cast)
- check_val_allowed(cast)
- check_val_disallowed(cast)
- end
- end
-
- # Check if the values to long are legal and raise if not.
- def check_val_long(cast)
- unless cast[:long].is_a? String and cast[:long].length > 1
- raise CastError, "Illegal cast of long: '#{cast[:long]}'"
- end
- end
-
- # Check if the values to short are legal and raise if not.
- def check_val_short(cast)
- unless cast[:short].is_a? String and cast[:short].length == 1
- raise CastError, "Illegal cast of short: '#{cast[:short]}'"
- end
- end
-
- # Check if values to type are legal and raise if not.
- def check_val_type(cast)
- type_hash = {}
- TYPES.each do |type|
- type_hash[type] = true
- end
-
- unless type_hash.has_key? cast[:type]
- raise CastError, "Illegal cast of type: '#{cast[:type]}'"
- end
- end
-
- # Check if values to mandatory are legal and raise if not.
- def check_val_mandatory(cast)
- unless cast[:mandatory] == true or cast[:mandatory] == false
- raise CastError, "Illegal cast of mandatory: '#{cast[:mandatory]}'"
- end
- end
-
- # Check if values to default are legal and raise if not.
- def check_val_default(cast)
- unless cast[:default].nil? or
- cast[:default].is_a? String or
- cast[:default].is_a? Integer or
- cast[:default].is_a? Float
- raise CastError, "Illegal cast of default: '#{cast[:default]}'"
- end
- end
-
- # Check if values to allowed are legal and raise if not.
- def check_val_allowed(cast)
- unless cast[:allowed].is_a? String or cast[:allowed].nil?
- raise CastError, "Illegal cast of allowed: '#{cast[:allowed]}'"
- end
- end
-
- # Check if values to disallowed are legal and raise if not.
- def check_val_disallowed(cast)
- unless cast[:disallowed].is_a? String or cast[:disallowed].nil?
- raise CastError, "Illegal cast of disallowed: '#{cast[:disallowed]}'"
- end
- end
-
- # Check cast for duplicate long or short options names.
- def check_duplicates
- check_hash = {}
- @cast_list.each do |cast|
- raise CastError, "Duplicate argument: '--#{cast[:long]}'" if check_hash.has_key? cast[:long]
- raise CastError, "Duplicate argument: '-#{cast[:short]}'" if check_hash.has_key? cast[:short]
- check_hash[cast[:long]] = true
- check_hash[cast[:short]] = true
- end
- end
-
- # Convert values to :long keys to symbols for all casts.
- def long_to_sym
- @cast_list.each do |cast|
- cast[:long] = cast[:long].to_sym
- end
- end
-
-end
-
-
-# Class for parsing argv using OptionParser according to given casts.
-# Default options are set, file glob expressions expanded, and options are
-# checked according to the casts. Usage information is printed and exit called
-# if required.
-class OptionHandler
- REGEX_LIST = /^(list|files|files!)$/
- REGEX_INT = /^(int|uint)$/
- REGEX_STRING = /^(file|file!|dir|dir!|genome)$/
-
- def initialize(argv, casts, script_path, test=nil)
- @argv = argv
- @casts = casts
- @script_path = script_path
- @test = test
- end
-
- # Parse options from argv using OptionParser and casts denoting long and
- # short option names. Usage information is printed and exit called.
- # A hash with options is returned.
- def options_parse
- @options = {}
-
- option_parser = OptionParser.new do |option|
- @casts.each do |cast|
- case cast[:type]
- when 'flag'
- option.on("-#{cast[:short]}", "--#{cast[:long]}") do |o|
- @options[cast[:long]] = o
- end
- when 'float'
- option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
- @options[cast[:long]] = f
- end
- when 'string'
- option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
- @options[cast[:long]] = s.to_sym # TODO: this to_sym - is that needed?
- end
- when REGEX_LIST
- option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
- @options[cast[:long]] = a
- end
- when REGEX_INT
- option.on("-#{cast[:short]}", "--#{cast[:long]} I", Integer) do |i|
- @options[cast[:long]] = i
- end
- when REGEX_STRING
- option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
- @options[cast[:long]] = s
- end
- else
- raise ArgumentError, "Unknown option type: '#{cast[:type]}'"
- end
- end
- end
-
- option_parser.parse!(@argv)
-
- if print_usage_full?
- print_usage_and_exit(true)
- elsif print_usage_short?
- print_usage_and_exit
- end
-
- options_default
- options_glob
- options_check
-
- @options
- end
-
- # Given the script name determine the path of the wiki file with the usage info.
- def wiki_path
- path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
- raise "No such wiki file: #{path}" unless File.file? path
- path
- end
-
- # Check if full "usage info" should be printed.
- def print_usage_full?
- @options[:help]
- end
-
- # Check if short "usage info" should be printed.
- def print_usage_short?
- if not $stdin.tty?
- return false
- elsif @options[:stream_in]
- return false
- elsif @options[:data_in]
- return false
- elsif wiki_path =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/ # TODO get rid of this!
- return false
- else
- return true
- end
- end
-
- # Print usage info by Calling an external script 'print_wiki'
- # using a system() call and exit. An optional 'full' flag
- # outputs the full usage info.
- def print_usage_and_exit(full=nil)
- if @test
- return
- else
- if full
- system("print_wiki --data_in #{wiki_path} --help")
- else
- system("print_wiki --data_in #{wiki_path}")
- end
-
- raise "Failed printing wiki: #{wiki_path}" unless $?.success?
-
- exit
- end
- end
-
- # Set default options value from cast unless a value is set.
- def options_default
- @casts.each do |cast|
- if cast[:default]
- unless @options.has_key? cast[:long]
- if cast[:type] == 'list'
- @options[cast[:long]] = cast[:default].split ','
- else
- @options[cast[:long]] = cast[:default]
- end
- end
- end
- end
- end
-
- # Expands glob expressions to a full list of paths.
- # Examples: "*.fna" or "foo.fna,*.fna" or "foo.fna,/bar/*.fna"
- def options_glob
- @casts.each do |cast|
- if cast[:type] == 'files' or cast[:type] == 'files!'
- if @options.has_key? cast[:long]
- files = []
-
- @options[cast[:long]].each do |path|
- if path.include? "*"
- Dir.glob(path).each do |file|
- files << file if File.file? file
- end
- else
- files << path
- end
- end
-
- @options[cast[:long]] = files
- end
- end
- end
- end
-
- # Check all options according to casts.
- def options_check
- @casts.each do |cast|
- options_check_mandatory(cast)
- options_check_int(cast)
- options_check_uint(cast)
- options_check_file(cast)
- options_check_files(cast)
- options_check_dir(cast)
- options_check_allowed(cast)
- options_check_disallowed(cast)
- end
- end
-
- # Check if a mandatory option is set and raise if it isn't.
- def options_check_mandatory(cast)
- if cast[:mandatory]
- raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
- end
- end
-
- # Check int type option and raise if not an integer.
- def options_check_int(cast)
- if cast[:type] == 'int' and @options.has_key? cast[:long]
- unless @options[cast[:long]].is_a? Integer
- raise ArgumentError, "Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"
- end
- end
- end
-
- # Check uint type option and raise if not an unsinged integer.
- def options_check_uint(cast)
- if cast[:type] == 'uint' and @options.has_key? cast[:long]
- unless @options[cast[:long]].is_a? Integer and @options[cast[:long]] >= 0
- raise ArgumentError, "Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"
- end
- end
- end
-
- # Check file! type argument and raise if file don't exists.
- def options_check_file(cast)
- if cast[:type] == 'file!' and @options.has_key? cast[:long]
- raise ArgumentError, "No such file: '#{@options[cast[:long]]}'" unless File.file? @options[cast[:long]]
- end
- end
-
- # Check files! type argument and raise if files don't exists.
- def options_check_files(cast)
- if cast[:type] == 'files!' and @options.has_key? cast[:long]
- @options[cast[:long]].each do |path|
- next if path == "-"
- raise ArgumentError, "File not readable: '#{path}'" unless File.readable? path
- end
- end
- end
-
- # Check dir! type argument and raise if directory don't exist.
- def options_check_dir(cast)
- if cast[:type] == 'dir!' and @options.has_key? cast[:long]
- raise ArgumentError, "No such directory: '#{@options[cast[:long]]}'" unless File.directory? @options[cast[:long]]
- end
- end
-
- # Check options and raise unless allowed.
- def options_check_allowed(cast)
- if cast[:allowed] and @options.has_key? cast[:long]
- allowed_hash = {}
- cast[:allowed].split(',').each { |a| allowed_hash[a.to_s] = 1 }
-
- raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed" unless allowed_hash.has_key? @options[cast[:long]].to_s
- end
- end
-
- # Check disallowed argument values and raise if disallowed.
- def options_check_disallowed(cast)
- if cast[:disallowed] and @options.has_key? cast[:long]
- cast[:disallowed].split(',').each do |val|
- raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed" if val.to_s == @options[cast[:long]].to_s
- end
- end
- end
-end
-
-# Class for manipulating the execution status of Biopieces by setting a
-# status file with a time stamp, process id, and command arguments. The
-# status file is used for creating log entries and for displaying the
-# runtime status of Biopieces.
-class Status
- # Write the status to a status file.
- def set
- time0 = Time.new.strftime("%Y-%m-%d %X")
-
- File.open(path, mode="w") do |fh|
- fh.puts [time0, ARGV.join(" ")].join(";")
- end
- end
-
- # Append the a temporary directory path to the status file.
- def set_tmpdir(tmpdir_path)
- status = ""
-
- File.open(path, mode="r") do |fh|
- status = fh.read.chomp
- end
-
- status = "#{status};#{tmpdir_path}\n"
-
- File.open(path, mode="w") do |fh|
- fh << status
- end
- end
-
- # Extract the temporary directory path from the status file,
- # and return this or nil if not found.
- def get_tmpdir
- File.open(path, mode="r") do |fh|
- tmpdir_path = fh.read.chomp.split(";").last
- return tmpdir_path if File.directory?(tmpdir_path)
- end
-
- nil
- end
-
- # Write the Biopiece status to the log file.
- def log(exit_status)
- time1 = Time.new.strftime("%Y-%m-%d %X")
- user = ENV["USER"]
- script = File.basename($0)
-
- stream = File.open(path)
- time0, args, tmp_dir = stream.first.split(";")
- stream.close
-
- elap = time_diff(time0, time1)
- command = [script, args].join(" ")
- log_file = ENV["BP_LOG"] + "/biopieces.log"
-
- File.open(log_file, mode = "a") { |file| file.puts [time0, time1, elap, user, exit_status, command].join("\t") }
- end
-
- # Delete status file.
- def delete
- File.delete(path)
- end
-
- private
-
- # Path to status file
- def path
- user = ENV["USER"]
- script = File.basename($0)
- pid = $$
- path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
- end
-
- # Get the elapsed time from the difference between two time stamps.
- def time_diff(t0, t1)
- Time.at((DateTime.parse(t1).to_time - DateTime.parse(t0).to_time).to_i).gmtime.strftime('%X')
- end
-end
-
-
-class Stream < IO
- # Open Biopieces output data stream for reading from stdin or a file
- # specified in options[:stream_in] OR writing to stdout or a file
- # specified in options[:stream_out] or options[:data_out].
- def self.open(options, mode, stdio)
- if mode == "r"
- if options[:data_in] and options[:data_in].first == "-"
- self.nread(["-"])
- else
- $stdin.tty? ? read(options[:stream_in]) : stdio
- end
- elsif mode == "w"
- options[:stream_out] ? self.write(options[:stream_out], options[:compress]) : stdio
- else
- raise "Bad mode #{mode}"
- end
- end
-
- private
-
- # Opens a reads stream to a list of files.
- def self.read(files)
- return if files.nil? #TODO case/when
- self.zipped?(files) ? self.zread(files) : self.nread(files)
- end
-
- # Opens a write stream to a file and returns a _io_ object.
- def self.write(file, zip=nil)
- zip ? self.zwrite(file) : self.nwrite(file)
- end
-
- # Opens a list of gzipped files for reading and return an _io_ object.
- def self.zread(files)
- stdin, stdout, stderr = Open3.popen3("zcat " + files.join(' '));
- stdin.close
- stderr.close
- stdout
- end
-
- # Opens a file for gzipped writing and return an _io_ object.
- def self.zwrite(file)
- stdin, stdout, stderr = Open3.popen3("gzip -f > #{file}")
- stderr.close
- stdout.close
- stdin
- end
-
- # Opens a list of files for reading and return an _io_ object.
- def self.nread(files)
- stdin, stdout, stderr = Open3.popen3("cat " + files.join(' '));
- stdin.close
- stderr.close
- stdout
- end
-
- # Opens a file for writing and return an _io_ object.
- def self.nwrite(file)
- File.open(file, mode="w")
- end
-
- # Test if a list of files are gzipped or not.
- # Raises if files are mixed zipped and unzipped.
- def self.zipped?(files)
- type_hash = {}
-
- files.each do |file|
- type = `file #{file}`
-
- if type =~ /gzip compressed/
- type_hash[:gzip] = true
- else
- type_hash[:ascii] = true
- end
- end
-
- raise "Mixture of zipped and unzipped files" if type_hash.size == 2
-
- type_hash[:gzip]
- end
-end
-
-
-Status.new.set
-
-at_exit do
- exit_status = $! ? $!.inspect : "OK"
-
- case exit_status
- when /error|errno/i
- exit_status = "ERROR"
- when "Interrupt"
- exit_status = "INTERRUPTED"
- when /SIGTERM/
- exit_status = "TERMINATED"
- when /SIGQUIT/
- exit_status = "QUIT"
- end
-
- status = Status.new
- tmpdir = status.get_tmpdir
- FileUtils.remove_entry_secure(tmpdir) unless tmpdir.nil?
- status.log(exit_status)
- status.delete
-end
-
-
-__END__
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-BitsInChar = 8
-
-# Error class for all exceptions to do with BitArray.
-class BitArrayError < StandardError; end
-
-# Class containing methods for creating and manipulating a bit array.
-class BitArray
- attr_reader :size, :byte_array
-
- # Method to initialize a new bit array of a given size.
- def initialize(size)
- @size = size
- @byte_array = init_byte_array
- @count_array = init_count_array
- end
-
- # Method to set a bit to 1 at a given position in the bit array.
- def bit_set(pos)
- raise BitArrayError, "Position #{pos} must be an integer." unless pos.is_a? Fixnum
- raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
-
- @byte_array[byte_pos(pos)] = (@byte_array[byte_pos(pos)].ord | bit_pos(pos)).chr
- end
-
- # Method to check if a bit at a given position in the bit array is set.
- def bit_set?(pos)
- raise BitArrayError, "Position #{pos} must be an integer." unless pos.is_a? Fixnum
- raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
-
- (@byte_array[byte_pos(pos)].ord & bit_pos(pos)) != 0
- end
-
- # Method that returns the number of bits set "on" in a bit array.
- def bits_on
- bits_on = 0
-
- (0 ... self.byte_array.size).each do |byte|
- bits_on += @count_array[self.byte_array[byte].ord]
- end
-
- bits_on
- end
-
- # Method that returns the number of bits set "off" in a bit array.
- def bits_off
- @size - bits_on
- end
-
- # Method to run bitwise AND (&) on two bit arrays and return the
- # result in a new bit array. Bits are copied if they exists in BOTH operands.
- # 00111100 & 00001101 = 00001100
- def &(ba)
- raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
-
- result = BitArray.new(ba.size)
-
- (0 ... ba.byte_array.size).each do |byte|
- result.byte_array[byte] = (self.byte_array[byte].ord & ba.byte_array[byte].ord).chr
- end
-
- result
- end
-
- # Method to run bitwise OR (|) on two bit arrays and return the
- # result in a new bit array. Bits are copied if they exists in EITHER operands.
- # 00111100 | 00001101 = 00111101
- def |(ba)
- raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
-
- result = BitArray.new(ba.size)
-
- (0 ... ba.byte_array.size).each do |byte|
- result.byte_array[byte] = (self.byte_array[byte].ord | ba.byte_array[byte].ord).chr
- end
-
- result
- end
-
- # Method to run bitwise XOR (^) on two bit arrays and return the
- # result in a new bit array. Bits are copied if they exists in ONE BUT NOT BOTH operands.
- # 00111100 ^ 00001101 = 00110001
- def ^(ba)
- raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
-
- result = BitArray.new(ba.size)
-
- (0 ... ba.byte_array.size).each do |byte|
- result.byte_array[byte] = (self.byte_array[byte].ord ^ ba.byte_array[byte].ord).chr
- end
-
- result
- end
-
- # Method to convert a bit array to a string.
- def to_s
- string = ""
-
- (0 ... @size).each do |pos|
- if self.bit_set? pos
- string << "1"
- else
- string << "0"
- end
- end
-
- string
- end
-
- alias :to_string :to_s
-
- private
-
- # Method to initialize the byte array (string) that constitutes the bit array.
- def init_byte_array
- raise BitArrayError, "Size must be an integer, not #{@size}" unless @size.is_a? Fixnum
- raise BitArrayError, "Size must be positive, not #{@size}" unless @size > 0
-
- byte_array = ""
- byte_array << 0.chr * (((@size - 1) / BitsInChar) + 1)
-
- byte_array
- end
-
- # Method that returns an array where the element index value is
- # the number of bits set for that index value.
- def init_count_array
- count_array = []
-
- (0 ... (2 ** BitsInChar)).each do |i|
- count_array << bits_in_char(i)
- end
-
- count_array
- end
-
- # Method that returns the number of set bits in a char.
- def bits_in_char(char)
- bits = 0
-
- (0 ... BitsInChar).each do |pos|
- bits += 1 if ((char & bit_pos(pos)) != 0)
- end
-
- bits
- end
-
- # Method that returns the byte position in the byte array for a given bit position.
- def byte_pos(pos)
- pos / BitsInChar
- end
-
- # Method that returns the bit position in a byte.
- def bit_pos(pos)
- 1 << (BitsInChar - 1 - (pos % BitsInChar))
- end
-end
-
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Error class for all exceptions to do with String.
-class StringError < StandardError; end
-
-# Monkey patching Class String to add bitwise operators.
-# Behaviour matching Perl's:
-# http://perldoc.perl.org/perlop.html#Bitwise-String-Operators
-class String
- # Method to that returns the case senstive Hamming Distance between two strings.
- # http://en.wikipedia.org/wiki/Hamming_distance
- def self.hamming_dist(str1, str2)
- raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}" if str1.length != str2.length
- (str1 ^ str2 ).count("\x01-\xff")
- end
-
- # Method that performs bitwise AND operation where bits
- # are copied if they exists in BOTH operands. If the operand
- # sizes are different, the & operator methods acts as though
- # the longer operand were truncated to the length of the shorter.
- def &(str)
- new = ""
-
- (0 ... [self.length, str.length].min).each do |i|
- new << (self[i].ord & str[i].ord)
- end
-
- new
- end
-
- # Method that performs bitwise OR operation where bits
- # are copied if they exists in EITHER operands. If the operand
- # sizes differ, the shorter operand is extended with the terminal
- # part of the longer operand.
- def |(str)
- new = ""
-
- min = [self.length, str.length].min
-
- (0 ... min).each do |i|
- new << (self[i].ord | str[i].ord)
- end
-
- if self.length > str.length
- new << self[min ... self.length]
- elsif self.length < str.length
- new << str[min ... str.length]
- end
-
- new
- end
-
- # Method that performs bitwise XOR operation where bits
- # are copied if they exists in ONE BUT NOT BOTH operands.
- def ^(str)
- new = ""
-
- (0 ... [self.length, str.length].min).each do |i|
- new << (self[i].ord ^ str[i].ord)
- end
-
- new
- end
-end
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Error class for all exceptions to do with Digest.
-class DigestError < StandardError; end
-
-class Digest
- include Enumerable
-
- # Initialize a digest object with the following arguments:
- # - seq: A sequence object.
- # - pattern: A restriction enzyme recognition pattern.
- # - cut_pos: Offset from match position where the enzyme cuts.
- def initialize(seq, pattern, cut_pos)
- @seq = seq
- @pattern = disambiguate(pattern)
- @cut_pos = cut_pos
- @offset = 0
- end
-
- # Method to get the next digestion product from a sequence.
- def each
- @seq.seq.upcase.scan @pattern do
- pos = $`.length + @cut_pos - 1
-
- if pos >= 0 and pos < @seq.length - 2
- seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{pos}]", @seq.seq[@offset .. pos], @seq.type)
-
- yield seq
- end
-
- @offset = pos + 1
- end
-
- if @offset < 0
- @offset = 0
- elsif @offset > @seq.length
- @offset = 0
- end
-
- seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]", @seq.seq[@offset .. @seq.length], @seq.type)
-
- yield seq
-
- self # conventionally
- end
-
- private
-
- # Method that returns a regexp object with a restriction
- # enzyme pattern with ambiguity codes substituted to the
- # appropriate regexp.
- def disambiguate(pattern)
- ambiguity = {
- 'A' => "A",
- 'T' => "T",
- 'U' => "T",
- 'C' => "C",
- 'G' => "G",
- 'M' => "[AC]",
- 'R' => "[AG]",
- 'W' => "[AT]",
- 'S' => "[CG]",
- 'Y' => "[CT]",
- 'K' => "[GT]",
- 'V' => "[ACG]",
- 'H' => "[ACT]",
- 'D' => "[AGT]",
- 'B' => "[CGT]",
- 'N' => "[GATC]"
- }
-
- new_pattern = ""
-
- pattern.upcase.each_char do |char|
- if ambiguity.has_key? char
- new_pattern << ambiguity[char]
- else
- raise DigestError, "Could not disambiguate residue: #{char}"
- end
- end
-
- Regexp.new(new_pattern)
- end
-end
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: Base36</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-
-</head>
-<body class="class">
-
- <div id="metadata">
- <div id="home-metadata">
- <div id="home-section" class="section">
- <h3 class="section-header">
- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
- </div>
- </div>
-
- <div id="file-metadata">
- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./base36_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="base36.rb">base36.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">Object</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
-
-
- <!-- Method Quickref -->
-
- <div id="method-list-section" class="section">
- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-decode">::decode</a></li>
-
- <li><a href="#method-c-encode">::encode</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
-
- </div>
-
- <div id="project-metadata">
-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
- </form>
-
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-
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- </div>
-
- <div id="documentation">
- <h1 class="class">Base36</h1>
-
- <div id="description">
- <p>
-Class containing methods to encode and decode Base 36. Note that the ALPH
-is [alph + num] and not [num + alph] which prevents us from simply using
-.to_i(36) and .to_s(36).
-</p>
-<p>
-<a
-href="http://en.wikipedia.org/wiki/Base_36">en.wikipedia.org/wiki/Base_36</a>
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="decode-method" class="method-detail ">
- <a name="method-c-decode"></a>
-
- <div class="method-heading">
-
- <span class="method-name">decode</span><span
- class="method-args">(base36)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that decodes a base36 string and returns an integer.
-</p>
-
-
-
- <div class="method-source-code"
- id="decode-source">
-<pre>
- <span class="ruby-comment cmt"># File base36.rb, line 55</span>
-55: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">decode</span>(<span class="ruby-identifier">base36</span>)
-56: <span class="ruby-identifier">raise</span> <span class="ruby-constant">Base36Error</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">empty?</span>
-57:
-58: <span class="ruby-identifier">result</span> = <span class="ruby-value">0</span>
-59: <span class="ruby-identifier">pos</span> = <span class="ruby-value">0</span>
-60:
-61: <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">reverse</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
-62: <span class="ruby-identifier">result</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">ALPH</span>.<span class="ruby-identifier">index</span>(<span class="ruby-identifier">char</span>) * (<span class="ruby-constant">BASE36</span> <span class="ruby-operator">**</span> <span class="ruby-identifier">pos</span>)
-63: <span class="ruby-identifier">pos</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-64: <span class="ruby-keyword kw">end</span>
-65:
-66: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">result</span>;
-67: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="encode-method" class="method-detail ">
- <a name="method-c-encode"></a>
-
- <div class="method-heading">
-
- <span class="method-name">encode</span><span
- class="method-args">(num)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that encodes an integer into a base36 string that is returned.
-</p>
-
-
-
- <div class="method-source-code"
- id="encode-source">
-<pre>
- <span class="ruby-comment cmt"># File base36.rb, line 39</span>
-39: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">encode</span>(<span class="ruby-identifier">num</span>)
-40: <span class="ruby-identifier">raise</span> <span class="ruby-constant">Base36Error</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">num</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
-41:
-42: <span class="ruby-identifier">base36</span> = <span class="ruby-value str">""</span>
-43:
-44: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">num</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
-45: <span class="ruby-identifier">base36</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">ALPH</span>[(<span class="ruby-identifier">num</span> <span class="ruby-operator">%</span> <span class="ruby-constant">BASE36</span>)]
-46: <span class="ruby-identifier">num</span> <span class="ruby-operator">/=</span> <span class="ruby-constant">BASE36</span>
-47: <span class="ruby-keyword kw">end</span>
-48:
-49: <span class="ruby-identifier">base36</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">ALPH</span>[<span class="ruby-value">0</span>] <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">num</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-50:
-51: <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">reverse</span>
-52: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
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-
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-
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- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
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- <h1 class="class">Biopieces</h1>
-
- <div id="description">
- <p>
-<a href="Biopieces.html">Biopieces</a> are command line scripts and uses
-OptionParser to parse command line options according to a list of casts.
-Each cast prescribes the long and short name of the option, the type, if it
-is mandatory, the default value, and allowed and disallowed values. An
-optional list of extra casts can be supplied, and the integrity of the
-casts are checked. Following the command line parsing, the options are
-checked according to the casts. Methods are also included for handling the
-parsing and emitting of Biopiece records, which are ASCII text records
-consisting of lines with a key/value pair separated by a colon and a white
-space ’: ’. Each record is separated by a line with three
-dashes ’—’.
-</p>
-
- </div>
-
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- <h3 class="section-header">Attributes</h3>
-
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- <a name="out"></a>
-
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-
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- <span class="method-name">out</span><span
- class="attribute-access-type">[RW]</span>
- </div>
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- <!-- Methods -->
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- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(test=nil, input=STDIN, output=STDOUT)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize a Biopiece and write the status to file. Options are for testing
-purposes only.
-</p>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 49</span>
-49: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">input</span>=<span class="ruby-constant">STDIN</span>, <span class="ruby-identifier">output</span>=<span class="ruby-constant">STDOUT</span>)
-50: <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
-51: <span class="ruby-ivar">@input</span> = <span class="ruby-identifier">input</span>
-52: <span class="ruby-ivar">@output</span> = <span class="ruby-identifier">output</span>
-53: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="each-method" class="method-detail method-alias">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- </div>
-
-
-
-
- <div class="aliases">
- Alias for: <a href="Biopieces.html#method-i-each_record">each_record</a>
- </div>
-
- </div>
-
-
- <div id="each-record-method" class="method-detail ">
- <a name="method-i-each_record"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each_record</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open Biopiece input stream if not open and iterate over all Biopiece
-records in the stream.
-</p>
-
-
-
- <div class="method-source-code"
- id="each-record-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 66</span>
-66: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_record</span>
-67: <span class="ruby-ivar">@in</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>, <span class="ruby-ivar">@input</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
-68: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">nil?</span>
-69:
-70: <span class="ruby-identifier">record</span> = {}
-71:
-72: <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
-73: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">line</span>
-74: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^([^:]+): (.*)$/</span>
-75: <span class="ruby-identifier">record</span>[<span class="ruby-node">$1</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-node">$2</span>
-76: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^---$/</span>
-77: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
-78: <span class="ruby-identifier">record</span> = {}
-79: <span class="ruby-keyword kw">else</span>
-80: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad record format: #{line}"</span>
-81: <span class="ruby-keyword kw">end</span>
-82: <span class="ruby-keyword kw">end</span>
-83:
-84: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
-85:
-86: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
-87: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
- <div class="aliases">
- Also aliased as: <a href="Biopieces.html#method-i-each">each</a>
- </div>
-
-
-
- </div>
-
-
- <div id="mktmpdir-method" class="method-detail ">
- <a name="method-i-mktmpdir"></a>
-
- <div class="method-heading">
-
- <span class="method-name">mktmpdir</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Create a temporary directory inside the ENV[“BP_TMP“] dir.
-</p>
-
-
-
- <div class="method-source-code"
- id="mktmpdir-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 106</span>
-106: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mktmpdir</span>
-107: <span class="ruby-identifier">time</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">now</span>.<span class="ruby-identifier">to_i</span>
-108: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
-109: <span class="ruby-identifier">pid</span> = <span class="ruby-identifier">$$</span>
-110: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_TMP"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/"</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">user</span>, <span class="ruby-identifier">time</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pid</span>, <span class="ruby-identifier">pid</span>, <span class="ruby-value str">"bp_tmp"</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"_"</span>)
-111: <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">mkdir</span>(<span class="ruby-identifier">path</span>)
-112: <span class="ruby-constant">Status</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">path</span>)
-113: <span class="ruby-identifier">path</span>
-114: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="parse-method" class="method-detail ">
- <a name="method-i-parse"></a>
-
- <div class="method-heading">
-
- <span class="method-name">parse</span><span
- class="method-args">(argv, cast_list=[], script_path=$0)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check the integrity of a list of casts, followed by parsion options from
-argv and finally checking the options according to the casts. Returns nil
-if argv is empty, otherwise an options hash.
-</p>
-
-
-
- <div class="method-source-code"
- id="parse-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 58</span>
-58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">parse</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">cast_list</span>=[], <span class="ruby-identifier">script_path</span>=<span class="ruby-identifier">$0</span>)
-59: <span class="ruby-identifier">casts</span> = <span class="ruby-constant">Casts</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">cast_list</span>)
-60: <span class="ruby-identifier">option_handler</span> = <span class="ruby-constant">OptionHandler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-ivar">@test</span>)
-61: <span class="ruby-ivar">@options</span> = <span class="ruby-identifier">option_handler</span>.<span class="ruby-identifier">options_parse</span>
-62: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="puts-method" class="method-detail ">
- <a name="method-i-puts"></a>
-
- <div class="method-heading">
-
- <span class="method-name">puts</span><span
- class="method-args">(record)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open Biopiece output stream if not open and puts record to the stream.
-</p>
-
-
-
- <div class="method-source-code"
- id="puts-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 92</span>
- 92: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
- 93: <span class="ruby-ivar">@out</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>, <span class="ruby-ivar">@output</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
- 94:
- 95: <span class="ruby-identifier">record</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>,<span class="ruby-identifier">value</span><span class="ruby-operator">|</span>
- 96: <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{key.to_s}: #{value}\n"</span>
- 97: <span class="ruby-keyword kw">end</span>
- 98:
- 99: <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-value str">"---\n"</span>
-100: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-s-method" class="method-detail ">
- <a name="method-i-to_s"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_s</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="to-s-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 102</span>
-102: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
-103: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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-
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- charset="utf-8"></script>
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- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
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- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./bitarray_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="bitarray.rb">bitarray.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">Object</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
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- <!-- Method Quickref -->
-
- <div id="method-list-section" class="section">
- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-new">::new</a></li>
-
- <li><a href="#method-i-%26">#&</a></li>
-
- <li><a href="#method-i-%5E">#^</a></li>
-
- <li><a href="#method-i-bit_pos">#bit_pos</a></li>
-
- <li><a href="#method-i-bit_set">#bit_set</a></li>
-
- <li><a href="#method-i-bit_set%3F">#bit_set?</a></li>
-
- <li><a href="#method-i-bits_in_char">#bits_in_char</a></li>
-
- <li><a href="#method-i-bits_off">#bits_off</a></li>
-
- <li><a href="#method-i-bits_on">#bits_on</a></li>
-
- <li><a href="#method-i-byte_pos">#byte_pos</a></li>
-
- <li><a href="#method-i-init_byte_array">#init_byte_array</a></li>
-
- <li><a href="#method-i-init_count_array">#init_count_array</a></li>
-
- <li><a href="#method-i-to_s">#to_s</a></li>
-
- <li><a href="#method-i-%7C">#|</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
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- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
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- class="quicksearch-field" />
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-
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-
- <li><a href="./Base36.html">Base36</a></li>
-
- <li><a href="./Base36Error.html">Base36Error</a></li>
-
- <li><a href="./Biopieces.html">Biopieces</a></li>
-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
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-
- <li><a href="./Casts.html">Casts</a></li>
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-
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- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
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-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">BitArray</h1>
-
- <div id="description">
- <p>
-Class containing methods for creating and manipulating a bit array.
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
- <div id="attribute-method-details" class="method-section section">
- <h3 class="section-header">Attributes</h3>
-
-
- <div id="size-attribute-method" class="method-detail">
- <a name="size"></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">size</span><span
- class="attribute-access-type">[R]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="byte-array-attribute-method" class="method-detail">
- <a name="byte_array"></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">byte_array</span><span
- class="attribute-access-type">[R]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- </div>
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(size)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to initialize a new bit array of a given size.
-</p>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 35</span>
-35: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">size</span>)
-36: <span class="ruby-ivar">@size</span> = <span class="ruby-identifier">size</span>
-37: <span class="ruby-ivar">@byte_array</span> = <span class="ruby-identifier">init_byte_array</span>
-38: <span class="ruby-ivar">@count_array</span> = <span class="ruby-identifier">init_count_array</span>
-39: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%26"></a>
-
- <div class="method-heading">
-
- <span class="method-name">&</span><span
- class="method-args">(ba)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to run bitwise AND (&) on two bit arrays and return the result
-in a new bit array. Bits are copied if they exists in BOTH operands.
-00111100 & 00001101 = 00001100
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 76</span>
-76: <span class="ruby-keyword kw">def</span> &(<span class="ruby-identifier">ba</span>)
-77: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
-78:
-79: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
-80:
-81: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
-82: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
-83: <span class="ruby-keyword kw">end</span>
-84:
-85: <span class="ruby-identifier">result</span>
-86: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%5E"></a>
-
- <div class="method-heading">
-
- <span class="method-name">^</span><span
- class="method-args">(ba)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to run bitwise XOR (^) on two bit arrays and return the result in a
-new bit array. Bits are copied if they exists in ONE BUT NOT BOTH operands.
-00111100 ^ 00001101 = 00110001
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 106</span>
-106: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">^</span>(<span class="ruby-identifier">ba</span>)
-107: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
-108:
-109: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
-110:
-111: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
-112: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
-113: <span class="ruby-keyword kw">end</span>
-114:
-115: <span class="ruby-identifier">result</span>
-116: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="bit-set-method" class="method-detail ">
- <a name="method-i-bit_set"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bit_set</span><span
- class="method-args">(pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to set a bit to 1 at a given position in the bit array.
-</p>
-
-
-
- <div class="method-source-code"
- id="bit-set-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 42</span>
-42: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_set</span>(<span class="ruby-identifier">pos</span>)
-43: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} must be an integer."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">pos</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
-44: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} outside of range: 0 ... #{@size}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span> ).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">pos</span>
-45:
-46: <span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)] = (<span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)).<span class="ruby-identifier">chr</span>
-47: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="bit-set--method" class="method-detail ">
- <a name="method-i-bit_set%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bit_set?</span><span
- class="method-args">(pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to check if a bit at a given position in the bit array is set.
-</p>
-
-
-
- <div class="method-source-code"
- id="bit-set--source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 50</span>
-50: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_set?</span>(<span class="ruby-identifier">pos</span>)
-51: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} must be an integer."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">pos</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
-52: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} outside of range: 0 ... #{@size}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span> ).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">pos</span>
-53:
-54: (<span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
-55: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="bits-off-method" class="method-detail ">
- <a name="method-i-bits_off"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bits_off</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the number of bits set “off” in a bit
-array.
-</p>
-
-
-
- <div class="method-source-code"
- id="bits-off-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 69</span>
-69: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_off</span>
-70: <span class="ruby-ivar">@size</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">bits_on</span>
-71: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="bits-on-method" class="method-detail ">
- <a name="method-i-bits_on"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bits_on</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the number of bits set “on” in a bit array.
-</p>
-
-
-
- <div class="method-source-code"
- id="bits-on-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 58</span>
-58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_on</span>
-59: <span class="ruby-identifier">bits_on</span> = <span class="ruby-value">0</span>
-60:
-61: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
-62: <span class="ruby-identifier">bits_on</span> <span class="ruby-operator">+=</span> <span class="ruby-ivar">@count_array</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>]
-63: <span class="ruby-keyword kw">end</span>
-64:
-65: <span class="ruby-identifier">bits_on</span>
-66: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-s-method" class="method-detail ">
- <a name="method-i-to_s"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_s</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to convert a bit array to a string.
-</p>
-
-
-
- <div class="method-source-code"
- id="to-s-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 119</span>
-119: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
-120: <span class="ruby-identifier">string</span> = <span class="ruby-value str">""</span>
-121:
-122: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pos</span><span class="ruby-operator">|</span>
-123: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bit_set?</span> <span class="ruby-identifier">pos</span>
-124: <span class="ruby-identifier">string</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"1"</span>
-125: <span class="ruby-keyword kw">else</span>
-126: <span class="ruby-identifier">string</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"0"</span>
-127: <span class="ruby-keyword kw">end</span>
-128: <span class="ruby-keyword kw">end</span>
-129:
-130: <span class="ruby-identifier">string</span>
-131: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%7C"></a>
-
- <div class="method-heading">
-
- <span class="method-name">|</span><span
- class="method-args">(ba)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to run bitwise OR (|) on two bit arrays and return the result in a
-new bit array. Bits are copied if they exists in EITHER operands. 00111100
-| 00001101 = 00111101
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 91</span>
- 91: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">|</span>(<span class="ruby-identifier">ba</span>)
- 92: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
- 93:
- 94: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
- 95:
- 96: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
- 97: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
- 98: <span class="ruby-keyword kw">end</span>
- 99:
-100: <span class="ruby-identifier">result</span>
-101: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="bit-pos-method" class="method-detail ">
- <a name="method-i-bit_pos"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bit_pos</span><span
- class="method-args">(pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the bit position in a byte.
-</p>
-
-
-
- <div class="method-source-code"
- id="bit-pos-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 177</span>
-177: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)
-178: <span class="ruby-value">1</span> <span class="ruby-operator"><<</span> (<span class="ruby-constant">BitsInChar</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">-</span> (<span class="ruby-identifier">pos</span> <span class="ruby-operator">%</span> <span class="ruby-constant">BitsInChar</span>))
-179: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="bits-in-char-method" class="method-detail ">
- <a name="method-i-bits_in_char"></a>
-
- <div class="method-heading">
-
- <span class="method-name">bits_in_char</span><span
- class="method-args">(char)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the number of set bits in a char.
-</p>
-
-
-
- <div class="method-source-code"
- id="bits-in-char-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 161</span>
-161: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_in_char</span>(<span class="ruby-identifier">char</span>)
-162: <span class="ruby-identifier">bits</span> = <span class="ruby-value">0</span>
-163:
-164: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-constant">BitsInChar</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pos</span><span class="ruby-operator">|</span>
-165: <span class="ruby-identifier">bits</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span> <span class="ruby-keyword kw">if</span> ((<span class="ruby-identifier">char</span> & <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>)
-166: <span class="ruby-keyword kw">end</span>
-167:
-168: <span class="ruby-identifier">bits</span>
-169: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="byte-pos-method" class="method-detail ">
- <a name="method-i-byte_pos"></a>
-
- <div class="method-heading">
-
- <span class="method-name">byte_pos</span><span
- class="method-args">(pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the byte position in the byte array for a given bit
-position.
-</p>
-
-
-
- <div class="method-source-code"
- id="byte-pos-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 172</span>
-172: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)
-173: <span class="ruby-identifier">pos</span> <span class="ruby-operator">/</span> <span class="ruby-constant">BitsInChar</span>
-174: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="init-byte-array-method" class="method-detail ">
- <a name="method-i-init_byte_array"></a>
-
- <div class="method-heading">
-
- <span class="method-name">init_byte_array</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to initialize the byte array (string) that constitutes the bit
-array.
-</p>
-
-
-
- <div class="method-source-code"
- id="init-byte-array-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 138</span>
-138: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">init_byte_array</span>
-139: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Size must be an integer, not #{@size}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@size</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
-140: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Size must be positive, not #{@size}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@size</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
-141:
-142: <span class="ruby-identifier">byte_array</span> = <span class="ruby-value str">""</span>
-143: <span class="ruby-identifier">byte_array</span> <span class="ruby-operator"><<</span> <span class="ruby-value">0</span>.<span class="ruby-identifier">chr</span> * (((<span class="ruby-ivar">@size</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>) <span class="ruby-operator">/</span> <span class="ruby-constant">BitsInChar</span>) <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
-144:
-145: <span class="ruby-identifier">byte_array</span>
-146: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="init-count-array-method" class="method-detail ">
- <a name="method-i-init_count_array"></a>
-
- <div class="method-heading">
-
- <span class="method-name">init_count_array</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns an array where the element index value is the number of
-bits set for that index value.
-</p>
-
-
-
- <div class="method-source-code"
- id="init-count-array-source">
-<pre>
- <span class="ruby-comment cmt"># File bitarray.rb, line 150</span>
-150: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">init_count_array</span>
-151: <span class="ruby-identifier">count_array</span> = []
-152:
-153: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> (<span class="ruby-value">2</span> <span class="ruby-operator">**</span> <span class="ruby-constant">BitsInChar</span>)).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
-154: <span class="ruby-identifier">count_array</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">bits_in_char</span>(<span class="ruby-identifier">i</span>)
-155: <span class="ruby-keyword kw">end</span>
-156:
-157: <span class="ruby-identifier">count_array</span>
-158: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
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- <h1 class="class">Boulder</h1>
-
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- <p>
-Class to manipulate boulder records - Lincoln Steins own YAML like format:
-<a
-href="http://stein.cshl.org/boulder/docs/Boulder.html">stein.cshl.org/boulder/docs/Boulder.html</a>
-</p>
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- <a name="method-c-new"></a>
-
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- <span class="method-name">new</span><span
- class="method-args">(input=STDIN, output=STDOUT)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize a <a href="Boulder.html">Boulder</a> object. Options are for
-testing purposes only.
-</p>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File boulder.rb, line 39</span>
-39: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">input</span>=<span class="ruby-constant">STDIN</span>, <span class="ruby-identifier">output</span>=<span class="ruby-constant">STDOUT</span>)
-40: <span class="ruby-ivar">@input</span> = <span class="ruby-identifier">input</span>
-41: <span class="ruby-ivar">@output</span> = <span class="ruby-identifier">output</span>
-42: <span class="ruby-keyword kw">end</span></pre>
- </div>
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- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
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-
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- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File boulder.rb, line 44</span>
-44: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
-45: <span class="ruby-keyword kw">while</span> <span class="ruby-keyword kw">not</span> <span class="ruby-ivar">@input</span>.<span class="ruby-identifier">eof?</span> <span class="ruby-keyword kw">do</span>
-46: <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@input</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-constant">SEP</span>)
-47: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing record seperator"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">block</span> <span class="ruby-operator">=~</span> <span class="ruby-node">/#{SEP}$/</span>
-48:
-49: <span class="ruby-identifier">record</span> = {}
-50:
-51: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp</span>(<span class="ruby-constant">SEP</span>).<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
-52: <span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">'='</span>, <span class="ruby-value">2</span>)
-53:
-54: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing key/value seperator"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">nil?</span>
-55: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing key"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">key</span>.<span class="ruby-identifier">empty?</span>
-56: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing value"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">empty?</span>
-57:
-58: <span class="ruby-identifier">record</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">val</span>
-59: <span class="ruby-keyword kw">end</span>
-60:
-61: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
-62: <span class="ruby-keyword kw">end</span>
-63: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-boulder-method" class="method-detail ">
- <a name="method-i-to_boulder"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_boulder</span><span
- class="method-args">(record)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that converts and returns a hash record as a <a
-href="Boulder.html">Boulder</a> string.
-</p>
-
-
-
- <div class="method-source-code"
- id="to-boulder-source">
-<pre>
- <span class="ruby-comment cmt"># File boulder.rb, line 67</span>
-67: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_boulder</span>(<span class="ruby-identifier">record</span>)
-68: <span class="ruby-identifier">str</span> = <span class="ruby-value str">""</span>
-69:
-70: <span class="ruby-identifier">record</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span><span class="ruby-operator">|</span>
-71: <span class="ruby-identifier">str</span> <span class="ruby-operator"><<</span> <span class="ruby-node">"#{key}=#{val}\n"</span>
-72: <span class="ruby-keyword kw">end</span>
-73:
-74: <span class="ruby-identifier">str</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"=\n"</span>
-75:
-76: <span class="ruby-identifier">str</span>
-77: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
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- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
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-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: BoulderError</title>
-
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-
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- charset="utf-8"></script>
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- class="thickbox" title="boulder.rb">boulder.rb</a></li>
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-Class to handle casts of command line options. Each cast prescribes the
-long and short name of the option, the type, if it is mandatory, the
-default value, and allowed and disallowed values. An optional list of extra
-casts can be supplied, and the integrity of the casts are checked.
-</p>
-
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-
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-
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- <dt><a name="MANDATORY">MANDATORY</a></dt>
-
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-
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- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(cast_list=[])</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize cast object with an optional options cast list to which
-ubiquitous casts are added after which all casts are checked.
-</p>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 132</span>
-132: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">cast_list</span>=[])
-133: <span class="ruby-ivar">@cast_list</span> = <span class="ruby-identifier">cast_list</span>
-134: <span class="ruby-identifier">ubiquitous</span>
-135: <span class="ruby-identifier">check</span>
-136: <span class="ruby-identifier">long_to_sym</span>
-137: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">push</span> *<span class="ruby-ivar">@cast_list</span>
-138: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="check-method" class="method-detail ">
- <a name="method-i-check"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check integrity of the casts.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 151</span>
-151: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check</span>
-152: <span class="ruby-identifier">check_keys</span>
-153: <span class="ruby-identifier">check_values</span>
-154: <span class="ruby-identifier">check_duplicates</span>
-155: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-duplicates-method" class="method-detail ">
- <a name="method-i-check_duplicates"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_duplicates</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check cast for duplicate long or short options names.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-duplicates-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 237</span>
-237: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_duplicates</span>
-238: <span class="ruby-identifier">check_hash</span> = {}
-239: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-240: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Duplicate argument: '--#{cast[:long]}'"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">check_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-241: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Duplicate argument: '-#{cast[:short]}'"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">check_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>]
-242: <span class="ruby-identifier">check_hash</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-keyword kw">true</span>
-243: <span class="ruby-identifier">check_hash</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>]] = <span class="ruby-keyword kw">true</span>
-244: <span class="ruby-keyword kw">end</span>
-245: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-keys-method" class="method-detail ">
- <a name="method-i-check_keys"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_keys</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if all mandatory keys are present in casts and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-keys-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 158</span>
-158: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_keys</span>
-159: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-160: <span class="ruby-constant">MANDATORY</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mandatory</span><span class="ruby-operator">|</span>
-161: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Missing symbol in cast: '#{mandatory.to_sym}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">mandatory</span>.<span class="ruby-identifier">to_sym</span>
-162: <span class="ruby-keyword kw">end</span>
-163: <span class="ruby-keyword kw">end</span>
-164: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-allowed-method" class="method-detail ">
- <a name="method-i-check_val_allowed"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_allowed</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if values to allowed are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-allowed-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 223</span>
-223: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_allowed</span>(<span class="ruby-identifier">cast</span>)
-224: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">nil?</span>
-225: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of allowed: '#{cast[:allowed]}'"</span>
-226: <span class="ruby-keyword kw">end</span>
-227: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-default-method" class="method-detail ">
- <a name="method-i-check_val_default"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_default</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if values to default are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-default-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 213</span>
-213: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_default</span>(<span class="ruby-identifier">cast</span>)
-214: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span>
-215: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span>
-216: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span> <span class="ruby-keyword kw">or</span>
-217: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Float</span>
-218: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of default: '#{cast[:default]}'"</span>
-219: <span class="ruby-keyword kw">end</span>
-220: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-disallowed-method" class="method-detail ">
- <a name="method-i-check_val_disallowed"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_disallowed</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if values to disallowed are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-disallowed-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 230</span>
-230: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_disallowed</span>(<span class="ruby-identifier">cast</span>)
-231: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">nil?</span>
-232: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of disallowed: '#{cast[:disallowed]}'"</span>
-233: <span class="ruby-keyword kw">end</span>
-234: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-long-method" class="method-detail ">
- <a name="method-i-check_val_long"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_long</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if the values to long are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-long-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 180</span>
-180: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_long</span>(<span class="ruby-identifier">cast</span>)
-181: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-value">1</span>
-182: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of long: '#{cast[:long]}'"</span>
-183: <span class="ruby-keyword kw">end</span>
-184: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-mandatory-method" class="method-detail ">
- <a name="method-i-check_val_mandatory"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_mandatory</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if values to mandatory are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-mandatory-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 206</span>
-206: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_mandatory</span>(<span class="ruby-identifier">cast</span>)
-207: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>] <span class="ruby-operator">==</span> <span class="ruby-keyword kw">true</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>] <span class="ruby-operator">==</span> <span class="ruby-keyword kw">false</span>
-208: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of mandatory: '#{cast[:mandatory]}'"</span>
-209: <span class="ruby-keyword kw">end</span>
-210: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-short-method" class="method-detail ">
- <a name="method-i-check_val_short"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_short</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if the values to short are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-short-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 187</span>
-187: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_short</span>(<span class="ruby-identifier">cast</span>)
-188: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>].<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
-189: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of short: '#{cast[:short]}'"</span>
-190: <span class="ruby-keyword kw">end</span>
-191: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-val-type-method" class="method-detail ">
- <a name="method-i-check_val_type"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_val_type</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if values to type are legal and raise if not.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-val-type-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 194</span>
-194: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_type</span>(<span class="ruby-identifier">cast</span>)
-195: <span class="ruby-identifier">type_hash</span> = {}
-196: <span class="ruby-constant">TYPES</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">type</span><span class="ruby-operator">|</span>
-197: <span class="ruby-identifier">type_hash</span>[<span class="ruby-identifier">type</span>] = <span class="ruby-keyword kw">true</span>
-198: <span class="ruby-keyword kw">end</span>
-199:
-200: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">type_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>]
-201: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of type: '#{cast[:type]}'"</span>
-202: <span class="ruby-keyword kw">end</span>
-203: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-values-method" class="method-detail ">
- <a name="method-i-check_values"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_values</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if all values in casts are valid.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-values-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 167</span>
-167: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_values</span>
-168: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-169: <span class="ruby-identifier">check_val_long</span>(<span class="ruby-identifier">cast</span>)
-170: <span class="ruby-identifier">check_val_short</span>(<span class="ruby-identifier">cast</span>)
-171: <span class="ruby-identifier">check_val_type</span>(<span class="ruby-identifier">cast</span>)
-172: <span class="ruby-identifier">check_val_mandatory</span>(<span class="ruby-identifier">cast</span>)
-173: <span class="ruby-identifier">check_val_default</span>(<span class="ruby-identifier">cast</span>)
-174: <span class="ruby-identifier">check_val_allowed</span>(<span class="ruby-identifier">cast</span>)
-175: <span class="ruby-identifier">check_val_disallowed</span>(<span class="ruby-identifier">cast</span>)
-176: <span class="ruby-keyword kw">end</span>
-177: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="long-to-sym-method" class="method-detail ">
- <a name="method-i-long_to_sym"></a>
-
- <div class="method-heading">
-
- <span class="method-name">long_to_sym</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Convert values to :long keys to symbols for all casts.
-</p>
-
-
-
- <div class="method-source-code"
- id="long-to-sym-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 248</span>
-248: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">long_to_sym</span>
-249: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-250: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>] = <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">to_sym</span>
-251: <span class="ruby-keyword kw">end</span>
-252: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="ubiquitous-method" class="method-detail ">
- <a name="method-i-ubiquitous"></a>
-
- <div class="method-heading">
-
- <span class="method-name">ubiquitous</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Add ubiquitous options casts.
-</p>
-
-
-
- <div class="method-source-code"
- id="ubiquitous-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 143</span>
-143: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">ubiquitous</span>
-144: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'help'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'?'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'flag'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
-145: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'stream_in'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'I'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'files!'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
-146: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'stream_out'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'O'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'file'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
-147: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'verbose'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'v'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'flag'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
-148: <span class="ruby-keyword kw">end</span></pre>
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-
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- <h1 class="class">Digest</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(seq, pattern, cut_pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize a digest object with the following arguments:
-</p>
-<ul>
-<li><p>
-seq: A sequence object.
-</p>
-</li>
-<li><p>
-pattern: A restriction enzyme recognition pattern.
-</p>
-</li>
-<li><p>
-cut_pos: Offset from match position where the enzyme cuts.
-</p>
-</li>
-</ul>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File digest.rb, line 37</span>
-37: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">seq</span>, <span class="ruby-identifier">pattern</span>, <span class="ruby-identifier">cut_pos</span>)
-38: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
-39: <span class="ruby-ivar">@pattern</span> = <span class="ruby-identifier">disambiguate</span>(<span class="ruby-identifier">pattern</span>)
-40: <span class="ruby-ivar">@cut_pos</span> = <span class="ruby-identifier">cut_pos</span>
-41: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
-42: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the next digestion product from a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File digest.rb, line 45</span>
-45: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
-46: <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span> <span class="ruby-ivar">@pattern</span> <span class="ruby-keyword kw">do</span>
-47: <span class="ruby-identifier">pos</span> = <span class="ruby-node">$`</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@cut_pos</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-48:
-49: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">>=</span> <span class="ruby-value">0</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">2</span>
-50: <span class="ruby-identifier">seq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">"#{@seq.seq_name}[#{@offset}-#{pos}]"</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-ivar">@offset</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">pos</span>], <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">type</span>)
-51:
-52: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">seq</span>
-53: <span class="ruby-keyword kw">end</span>
-54:
-55: <span class="ruby-ivar">@offset</span> = <span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
-56: <span class="ruby-keyword kw">end</span>
-57:
-58: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@offset</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
-59: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
-60: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@offset</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span>
-61: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
-62: <span class="ruby-keyword kw">end</span>
-63:
-64: <span class="ruby-identifier">seq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">"#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]"</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-ivar">@offset</span> <span class="ruby-operator">..</span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span>], <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">type</span>)
-65:
-66: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">seq</span>
-67:
-68: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
-69: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="disambiguate-method" class="method-detail ">
- <a name="method-i-disambiguate"></a>
-
- <div class="method-heading">
-
- <span class="method-name">disambiguate</span><span
- class="method-args">(pattern)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns a regexp object with a restriction enzyme pattern with
-ambiguity codes substituted to the appropriate regexp.
-</p>
-
-
-
- <div class="method-source-code"
- id="disambiguate-source">
-<pre>
- <span class="ruby-comment cmt"># File digest.rb, line 76</span>
- 76: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">disambiguate</span>(<span class="ruby-identifier">pattern</span>)
- 77: <span class="ruby-identifier">ambiguity</span> = {
- 78: <span class="ruby-value str">'A'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"A"</span>,
- 79: <span class="ruby-value str">'T'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"T"</span>,
- 80: <span class="ruby-value str">'U'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"T"</span>,
- 81: <span class="ruby-value str">'C'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"C"</span>,
- 82: <span class="ruby-value str">'G'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"G"</span>,
- 83: <span class="ruby-value str">'M'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AC]"</span>,
- 84: <span class="ruby-value str">'R'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AG]"</span>,
- 85: <span class="ruby-value str">'W'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AT]"</span>,
- 86: <span class="ruby-value str">'S'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CG]"</span>,
- 87: <span class="ruby-value str">'Y'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CT]"</span>,
- 88: <span class="ruby-value str">'K'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[GT]"</span>,
- 89: <span class="ruby-value str">'V'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[ACG]"</span>,
- 90: <span class="ruby-value str">'H'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[ACT]"</span>,
- 91: <span class="ruby-value str">'D'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AGT]"</span>,
- 92: <span class="ruby-value str">'B'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CGT]"</span>,
- 93: <span class="ruby-value str">'N'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[GATC]"</span>
- 94: }
- 95:
- 96: <span class="ruby-identifier">new_pattern</span> = <span class="ruby-value str">""</span>
- 97:
- 98: <span class="ruby-identifier">pattern</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
- 99: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">ambiguity</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">char</span>
-100: <span class="ruby-identifier">new_pattern</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">ambiguity</span>[<span class="ruby-identifier">char</span>]
-101: <span class="ruby-keyword kw">else</span>
-102: <span class="ruby-identifier">raise</span> <span class="ruby-constant">DigestError</span>, <span class="ruby-node">"Could not disambiguate residue: #{char}"</span>
-103: <span class="ruby-keyword kw">end</span>
-104: <span class="ruby-keyword kw">end</span>
-105:
-106: <span class="ruby-constant">Regexp</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">new_pattern</span>)
-107: <span class="ruby-keyword kw">end</span></pre>
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-
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-
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-
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-
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-
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-
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-
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-
- <li><a href="./Stream.html">Stream</a></li>
-
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-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">Fasta</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="get-entry-method" class="method-detail ">
- <a name="method-i-get_entry"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_entry</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the next FASTA entry form an ios and return this as a <a
-href="Seq.html">Seq</a> object. If no entry is found or eof then nil is
-returned.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-entry-source">
-<pre>
- <span class="ruby-comment cmt"># File fasta.rb, line 34</span>
-34: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
-35: <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
-36: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
-37:
-38: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
-39:
-40: (<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>) = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span>(<span class="ruby-identifier">$/</span>, <span class="ruby-value">2</span>)
-41:
-42: <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-43:
-44: <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
-45: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">type</span> = <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">?</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">downcase</span>
-46: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp re">/\s/</span>, <span class="ruby-value str">''</span>)
-47: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span> = <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/^>/</span>, <span class="ruby-value str">''</span>).<span class="ruby-identifier">rstrip</span>
-48:
-49: <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">empty?</span>
-50: <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">empty?</span>
-51:
-52: <span class="ruby-identifier">entry</span>
-53: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="puts-method" class="method-detail ">
- <a name="method-i-puts"></a>
-
- <div class="method-heading">
-
- <span class="method-name">puts</span><span
- class="method-args">(record)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-TODO - this should be some custom to_s method instead.
-</p>
-
-
-
- <div class="method-source-code"
- id="puts-source">
-<pre>
- <span class="ruby-comment cmt"># File fasta.rb, line 56</span>
-56: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
-57: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ_NAME</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ</span>
-58: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">">#{record[:SEQ_NAME]}\n"</span>
-59: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{record[:SEQ]}\n"</span>
-60: <span class="ruby-keyword kw">end</span>
-61: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-Error class for all exceptions to do with FASTA.
-</p>
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- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
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-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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- <h3 class="section-header">Methods</h3>
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-
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-
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-
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-
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-
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-
- <div id="documentation">
- <h1 class="class">Fastq</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="get-entry-method" class="method-detail ">
- <a name="method-i-get_entry"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_entry</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the next FASTQ entry form an ios and return this as a <a
-href="Seq.html">Seq</a> object. If no entry is found or eof then nil is
-returned.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-entry-source">
-<pre>
- <span class="ruby-comment cmt"># File fastq.rb, line 34</span>
-34: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
-35: <span class="ruby-keyword kw">begin</span>
-36: <span class="ruby-identifier">seq_name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
-37: <span class="ruby-identifier">seq</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
-38: <span class="ruby-identifier">qual_name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
-39: <span class="ruby-identifier">qual</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
-40:
-41: <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
-42: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">type</span> = <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">?</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">downcase</span>
-43: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span>
-44: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span> = <span class="ruby-identifier">seq_name</span>[<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">length</span>]
-45: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-identifier">qual</span>
-46:
-47: <span class="ruby-identifier">entry</span>
-48: <span class="ruby-keyword kw">rescue</span>
-49: <span class="ruby-keyword kw">nil</span>
-50: <span class="ruby-keyword kw">end</span>
-51: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="puts-method" class="method-detail ">
- <a name="method-i-puts"></a>
-
- <div class="method-heading">
-
- <span class="method-name">puts</span><span
- class="method-args">(record)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-TODO - this should be some custom to_s method instead.
-</p>
-
-
-
- <div class="method-source-code"
- id="puts-source">
-<pre>
- <span class="ruby-comment cmt"># File fastq.rb, line 54</span>
-54: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
-55: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ_NAME</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ</span>
-56: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">">#{record[:SEQ_NAME]}\n"</span>
-57: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{record[:SEQ]}\n"</span>
-58: <span class="ruby-keyword kw">end</span>
-59: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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- <p>
-Error class for all exceptions to do with FASTQ.
-</p>
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-
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-
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- <!-- Methods -->
-
-
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-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
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- Rdoc Generator</a> 1.1.6</small>.</p>
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-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
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- class="thickbox" title="filesys.rb">filesys.rb</a></li>
-
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-
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-
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- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-new">::new</a></li>
-
- <li><a href="#method-c-open">::open</a></li>
-
- <li><a href="#method-c-zopen">::zopen</a></li>
-
- <li><a href="#method-i-close">#close</a></li>
-
- <li><a href="#method-i-each">#each</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
-
- <div id="includes-section" class="section">
- <h3 class="section-header">Included Modules</h3>
- <ul class="link-list">
-
-
- <li><span class="include">Enumerable</span></li>
-
-
- </ul>
- </div>
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-
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- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
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-
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-
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-
- <li><a href="./FilesysError.html">FilesysError</a></li>
-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
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-
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-
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- <div id="documentation">
- <h1 class="class">Filesys</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(io, type=nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File filesys.rb, line 58</span>
-58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>, <span class="ruby-identifier">type</span>=<span class="ruby-keyword kw">nil</span>)
-59: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
-60: <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
-61: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="open-method" class="method-detail ">
- <a name="method-c-open"></a>
-
- <div class="method-heading">
-
- <span class="method-name">open</span><span
- class="method-args">(*args)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Class method allowing open to be used on (zipped) files. See File.open.
-</p>
-
-
-
- <div class="method-source-code"
- id="open-source">
-<pre>
- <span class="ruby-comment cmt"># File filesys.rb, line 35</span>
-35: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
-36: <span class="ruby-identifier">args</span> = *<span class="ruby-identifier">args</span>
-37: <span class="ruby-identifier">file</span> = <span class="ruby-identifier">args</span>.<span class="ruby-identifier">first</span>
-38:
-39: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">file</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
-40: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">STDIN</span>)
-41: <span class="ruby-keyword kw">elsif</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">pipe?</span> <span class="ruby-identifier">file</span>
-42: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>))
-43: <span class="ruby-keyword kw">else</span>
-44: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
-45: <span class="ruby-keyword kw">end</span>
-46:
-47: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
-48: <span class="ruby-keyword kw">begin</span>
-49: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">ios</span>
-50: <span class="ruby-keyword kw">ensure</span>
-51: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
-52: <span class="ruby-keyword kw">end</span>
-53: <span class="ruby-keyword kw">else</span>
-54: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">ios</span>
-55: <span class="ruby-keyword kw">end</span>
-56: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-class-method-details" class="method-section section">
- <h3 class="section-header">Private Class Methods</h3>
-
-
- <div id="zopen-method" class="method-detail ">
- <a name="method-c-zopen"></a>
-
- <div class="method-heading">
-
- <span class="method-name">zopen</span><span
- class="method-args">(*args)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Helper method to return an ios to a file that may be zipped in which case
-the ios is unzipped on the fly. See File.open.
-</p>
-
-
-
- <div class="method-source-code"
- id="zopen-source">
-<pre>
- <span class="ruby-comment cmt"># File filesys.rb, line 79</span>
-79: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
-80: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
-81:
-82: <span class="ruby-keyword kw">begin</span>
-83: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">Zlib</span><span class="ruby-operator">::</span><span class="ruby-constant">GzipReader</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
-84: <span class="ruby-keyword kw">rescue</span>
-85: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">rewind</span>
-86: <span class="ruby-keyword kw">end</span>
-87:
-88: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
-89: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="close-method" class="method-detail ">
- <a name="method-i-close"></a>
-
- <div class="method-heading">
-
- <span class="method-name">close</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to close ios.
-</p>
-
-
-
- <div class="method-source-code"
- id="close-source">
-<pre>
- <span class="ruby-comment cmt"># File filesys.rb, line 64</span>
-64: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
-65: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
-66: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Iterator method for parsing entries.
-</p>
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File filesys.rb, line 69</span>
-69: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
-70: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
-71: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">entry</span>
-72: <span class="ruby-keyword kw">end</span>
-73: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
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-Error class for all exceptions to do with <a
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-</p>
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+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="genbank.rb">genbank.rb</a></li>
-
- </ul>
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- </div>
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- <h3 class="section-header">Parent</h3>
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-
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- <h3 class="section-header">Methods</h3>
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-
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-
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-
- <li><a href="#method-i-get_keys">#get_keys</a></li>
-
- <li><a href="#method-i-get_seq">#get_seq</a></li>
-
- <li><a href="#method-i-want_key%3F">#want_key?</a></li>
-
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- height="16" width="16" alt="[+]"
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- <h1 class="class">Genbank</h1>
-
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-
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-
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-
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-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(io)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 32</span>
-32: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>)
-33: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
-34: <span class="ruby-ivar">@entry</span> = []
-35: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">(hash_keys, hash_feats, hash_quals)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Iterator method for parsing <a href="Genbank.html">Genbank</a> entries.
-</p>
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 38</span>
-38: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
-39: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
-40: <span class="ruby-identifier">keys</span> = <span class="ruby-identifier">get_keys</span>(<span class="ruby-identifier">hash_keys</span>)
-41: <span class="ruby-identifier">seq</span> = <span class="ruby-identifier">get_seq</span>
-42:
-43: <span class="ruby-identifier">features</span> = <span class="ruby-constant">GenbankFeatures</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@entry</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
-44:
-45: <span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">record</span><span class="ruby-operator">|</span>
-46: <span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each_pair</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>,<span class="ruby-identifier">val</span><span class="ruby-operator">|</span> <span class="ruby-identifier">record</span>[<span class="ruby-identifier">key</span>] = <span class="ruby-identifier">val</span> }
-47:
-48: <span class="ruby-identifier">loc</span> = <span class="ruby-constant">Locator</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">record</span>[<span class="ruby-value">:LOCATOR</span>], <span class="ruby-identifier">seq</span>)
-49: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">subseq</span>.<span class="ruby-identifier">seq</span>
-50: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">subseq</span>.<span class="ruby-identifier">length</span>
-51: <span class="ruby-identifier">record</span>[<span class="ruby-value">:STRAND</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">strand</span>
-52: <span class="ruby-identifier">record</span>[<span class="ruby-value">:S_BEG</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">s_beg</span>
-53: <span class="ruby-identifier">record</span>[<span class="ruby-value">:S_END</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">s_end</span>
-54:
-55: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
-56: <span class="ruby-keyword kw">end</span>
-57: <span class="ruby-keyword kw">end</span>
-58: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="get-entry-method" class="method-detail ">
- <a name="method-i-get_entry"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_entry</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the next <a href="Genbank.html">Genbank</a> entry form an ios
-and return this.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-entry-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 63</span>
-63: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
-64: <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-value str">"//"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">$/</span>)
-65: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
-66:
-67: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-value str">"//"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">$/</span> )
-68:
-69: <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span> <span class="ruby-identifier">$/</span>
-70:
-71: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">empty?</span>
-72:
-73: <span class="ruby-identifier">entry</span>
-74: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="get-keys-method" class="method-detail ">
- <a name="method-i-get_keys"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_keys</span><span
- class="method-args">(hash_keys)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the base keys from <a href="Genbank.html">Genbank</a> entry
-and return these in a hash.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-keys-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 93</span>
- 93: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_keys</span>(<span class="ruby-identifier">hash_keys</span>)
- 94: <span class="ruby-identifier">keys</span> = {}
- 95: <span class="ruby-identifier">i</span> = <span class="ruby-value">0</span>
- 96: <span class="ruby-identifier">j</span> = <span class="ruby-value">0</span>
- 97:
- 98: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^FEATURES/</span>
- 99: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{0,3}([A-Z]{2})/</span>
-100: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_key?</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-node">$1</span>)
-101: <span class="ruby-identifier">j</span> = <span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
-102:
-103: <span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\s+/</span>, <span class="ruby-value">2</span>)
-104:
-105: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^\s{0,3}[A-Z]/</span>
-106: <span class="ruby-identifier">val</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>].<span class="ruby-identifier">lstrip</span>
-107: <span class="ruby-identifier">j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-108: <span class="ruby-keyword kw">end</span>
-109:
-110: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>]
-111: <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] <span class="ruby-operator"><<</span> <span class="ruby-value str">";"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">val</span>
-112: <span class="ruby-keyword kw">else</span>
-113: <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">val</span>
-114: <span class="ruby-keyword kw">end</span>
-115: <span class="ruby-keyword kw">end</span>
-116: <span class="ruby-keyword kw">end</span>
-117:
-118: <span class="ruby-identifier">j</span> <span class="ruby-operator">></span> <span class="ruby-identifier">i</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">i</span> = <span class="ruby-identifier">j</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-119: <span class="ruby-keyword kw">end</span>
-120:
-121: <span class="ruby-identifier">keys</span>
-122: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="get-seq-method" class="method-detail ">
- <a name="method-i-get_seq"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_seq</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the DNA sequence from a <a href="Genbank.html">Genbank</a>
-entry and return this as a <a href="Seq.html">Seq</a> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-seq-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 78</span>
-78: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_seq</span>
-79: <span class="ruby-identifier">i</span> = <span class="ruby-ivar">@entry</span>.<span class="ruby-identifier">size</span>
-80: <span class="ruby-identifier">j</span> = <span class="ruby-identifier">i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-81:
-82: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^[A-Z]/</span>
-83: <span class="ruby-identifier">j</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
-84: <span class="ruby-keyword kw">end</span>
-85:
-86: <span class="ruby-identifier">seq</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">i</span>].<span class="ruby-identifier">join</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">" 0123456789"</span>)
-87:
-88: <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">seq</span>, <span class="ruby-value str">"dna"</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq</span>
-89: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="want-key--method" class="method-detail ">
- <a name="method-i-want_key%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">want_key?</span><span
- class="method-args">(hash_keys, key)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="want-key--source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 124</span>
-124: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_key?</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-identifier">key</span>)
-125: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hash_keys</span>
-126: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hash_keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>]
-127: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-128: <span class="ruby-keyword kw">else</span>
-129: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-130: <span class="ruby-keyword kw">end</span>
-131: <span class="ruby-keyword kw">else</span>
-132: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-133: <span class="ruby-keyword kw">end</span>
-134: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: GenbankError</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
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- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-
-</head>
-<body class="class">
-
- <div id="metadata">
- <div id="home-metadata">
- <div id="home-section" class="section">
- <h3 class="section-header">
- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
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- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="genbank.rb">genbank.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">StandardError</p>
-
- </div>
-
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-
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- <!-- Method Quickref -->
-
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- <!-- Included Modules -->
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-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
- </form>
-
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-
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-
- <li><a href="./Base36Error.html">Base36Error</a></li>
-
- <li><a href="./Biopieces.html">Biopieces</a></li>
-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
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-
- <li><a href="./Casts.html">Casts</a></li>
-
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-
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-
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-
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-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
- <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
-
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-
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-
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-
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-
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-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">GenbankError</h1>
-
- <div id="description">
- <p>
-Error class for all exceptions to do with <a
-href="Genbank.html">Genbank</a>.
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: GenbankFeatures</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
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- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-
-</head>
-<body class="class">
-
- <div id="metadata">
- <div id="home-metadata">
- <div id="home-section" class="section">
- <h3 class="section-header">
- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
- </div>
- </div>
-
- <div id="file-metadata">
- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="genbank.rb">genbank.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">Object</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
-
-
- <!-- Method Quickref -->
-
- <div id="method-list-section" class="section">
- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-new">::new</a></li>
-
- <li><a href="#method-i-each">#each</a></li>
-
- <li><a href="#method-i-get_quals">#get_quals</a></li>
-
- <li><a href="#method-i-want_feat%3F">#want_feat?</a></li>
-
- <li><a href="#method-i-want_qual%3F">#want_qual?</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
-
- </div>
-
- <div id="project-metadata">
-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
- </form>
-
- <ul class="link-list">
-
- <li><a href="./Base36.html">Base36</a></li>
-
- <li><a href="./Base36Error.html">Base36Error</a></li>
-
- <li><a href="./Biopieces.html">Biopieces</a></li>
-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
- <li><a href="./CastError.html">CastError</a></li>
-
- <li><a href="./Casts.html">Casts</a></li>
-
- <li><a href="./Digest.html">Digest</a></li>
-
- <li><a href="./DigestError.html">DigestError</a></li>
-
- <li><a href="./Fasta.html">Fasta</a></li>
-
- <li><a href="./FastaError.html">FastaError</a></li>
-
- <li><a href="./Fastq.html">Fastq</a></li>
-
- <li><a href="./FastqError.html">FastqError</a></li>
-
- <li><a href="./Filesys.html">Filesys</a></li>
-
- <li><a href="./FilesysError.html">FilesysError</a></li>
-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
- <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
-
- <li><a href="./Locator.html">Locator</a></li>
-
- <li><a href="./LocatorError.html">LocatorError</a></li>
-
- <li><a href="./OptionHandler.html">OptionHandler</a></li>
-
- <li><a href="./Read.html">Read</a></li>
-
- <li><a href="./SFF.html">SFF</a></li>
-
- <li><a href="./SFFError.html">SFFError</a></li>
-
- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">GenbankFeatures</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(entry, hash_feats, hash_quals)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 141</span>
-141: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">entry</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
-142: <span class="ruby-ivar">@entry</span> = <span class="ruby-identifier">entry</span>
-143: <span class="ruby-ivar">@hash_feats</span> = <span class="ruby-identifier">hash_feats</span>
-144: <span class="ruby-ivar">@hash_quals</span> = <span class="ruby-identifier">hash_quals</span>
-145: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 147</span>
-147: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
-148: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^ORIGIN/</span>
-149: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{5}([A-Za-z_-]+)/</span>
-150: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_feat?</span> <span class="ruby-node">$1</span>
-151: <span class="ruby-identifier">record</span> = {}
-152:
-153: <span class="ruby-identifier">feat</span>, <span class="ruby-identifier">loc</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\s+/</span>, <span class="ruby-value">2</span>)
-154:
-155: <span class="ruby-identifier">@@j</span> = <span class="ruby-identifier">@@i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
-156:
-157: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/</span>
-158: <span class="ruby-identifier">loc</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>].<span class="ruby-identifier">lstrip</span>
-159: <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-160: <span class="ruby-keyword kw">end</span>
-161:
-162: <span class="ruby-identifier">get_quals</span>.<span class="ruby-identifier">each_pair</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
-163: <span class="ruby-identifier">record</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>
-164: }
-165:
-166: <span class="ruby-identifier">record</span>[<span class="ruby-value">:FEATURE</span>] = <span class="ruby-identifier">feat</span>
-167: <span class="ruby-identifier">record</span>[<span class="ruby-value">:LOCATOR</span>] = <span class="ruby-identifier">loc</span>
-168:
-169: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
-170: <span class="ruby-keyword kw">end</span>
-171: <span class="ruby-keyword kw">end</span>
-172:
-173: <span class="ruby-identifier">@@j</span> <span class="ruby-operator">></span> <span class="ruby-identifier">@@i</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">@@i</span> = <span class="ruby-identifier">@@j</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">@@i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-174: <span class="ruby-keyword kw">end</span>
-175: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="get-quals-method" class="method-detail ">
- <a name="method-i-get_quals"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_quals</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="get-quals-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 179</span>
-179: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_quals</span>
-180: <span class="ruby-identifier">quals</span> = {}
-181: <span class="ruby-identifier">k</span> = <span class="ruby-value">0</span>
-182:
-183: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^\s{5}[A-Za-z_-]|^[A-Z]/</span>
-184: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{21}\/([^=]+)="([^"]+)/</span>
-185: <span class="ruby-identifier">qual</span> = <span class="ruby-node">$1</span>
-186: <span class="ruby-identifier">val</span> = <span class="ruby-node">$2</span>
-187:
-188: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_qual?</span> <span class="ruby-identifier">qual</span>
-189: <span class="ruby-identifier">k</span> = <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
-190:
-191: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/</span>
-192: <span class="ruby-identifier">val</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">chomp</span>(<span class="ruby-value str">'"'</span>)
-193: <span class="ruby-identifier">k</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-194: <span class="ruby-keyword kw">end</span>
-195:
-196: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>]
-197: <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>] <span class="ruby-operator"><<</span> <span class="ruby-value str">";"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">val</span>
-198: <span class="ruby-keyword kw">else</span>
-199: <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>] = <span class="ruby-identifier">val</span>
-200: <span class="ruby-keyword kw">end</span>
-201: <span class="ruby-keyword kw">end</span>
-202: <span class="ruby-keyword kw">end</span>
-203:
-204: <span class="ruby-identifier">k</span> <span class="ruby-operator">></span> <span class="ruby-identifier">@@j</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">@@j</span> = <span class="ruby-identifier">k</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-205: <span class="ruby-keyword kw">end</span>
-206:
-207: <span class="ruby-identifier">quals</span>
-208: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="want-feat--method" class="method-detail ">
- <a name="method-i-want_feat%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">want_feat?</span><span
- class="method-args">(feat)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="want-feat--source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 210</span>
-210: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_feat?</span>(<span class="ruby-identifier">feat</span>)
-211: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_feats</span>
-212: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_feats</span>[<span class="ruby-identifier">feat</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>]
-213: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-214: <span class="ruby-keyword kw">else</span>
-215: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-216: <span class="ruby-keyword kw">end</span>
-217: <span class="ruby-keyword kw">else</span>
-218: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-219: <span class="ruby-keyword kw">end</span>
-220: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="want-qual--method" class="method-detail ">
- <a name="method-i-want_qual%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">want_qual?</span><span
- class="method-args">(qual)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="want-qual--source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 222</span>
-222: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_qual?</span>(<span class="ruby-identifier">qual</span>)
-223: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_quals</span>
-224: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_quals</span>[<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>]
-225: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-226: <span class="ruby-keyword kw">else</span>
-227: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-228: <span class="ruby-keyword kw">end</span>
-229: <span class="ruby-keyword kw">else</span>
-230: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-231: <span class="ruby-keyword kw">end</span>
-232: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
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-
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- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
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-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: Locator</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
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- charset="utf-8"></script>
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- charset="utf-8"></script>
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- charset="utf-8"></script>
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- charset="utf-8"></script>
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-<body class="class">
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- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
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- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="genbank.rb">genbank.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">Object</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
-
-
- <!-- Method Quickref -->
-
- <div id="method-list-section" class="section">
- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-new">::new</a></li>
-
- <li><a href="#method-i-balance_parens%3F">#balance_parens?</a></li>
-
- <li><a href="#method-i-parse_locator">#parse_locator</a></li>
-
- <li><a href="#method-i-s_beg">#s_beg</a></li>
-
- <li><a href="#method-i-s_end">#s_end</a></li>
-
- <li><a href="#method-i-strand">#strand</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
-
- </div>
-
- <div id="project-metadata">
-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
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-
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-
- <li><a href="./Base36.html">Base36</a></li>
-
- <li><a href="./Base36Error.html">Base36Error</a></li>
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-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
- <li><a href="./CastError.html">CastError</a></li>
-
- <li><a href="./Casts.html">Casts</a></li>
-
- <li><a href="./Digest.html">Digest</a></li>
-
- <li><a href="./DigestError.html">DigestError</a></li>
-
- <li><a href="./Fasta.html">Fasta</a></li>
-
- <li><a href="./FastaError.html">FastaError</a></li>
-
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-
- <li><a href="./FastqError.html">FastqError</a></li>
-
- <li><a href="./Filesys.html">Filesys</a></li>
-
- <li><a href="./FilesysError.html">FilesysError</a></li>
-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
- <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
-
- <li><a href="./Locator.html">Locator</a></li>
-
- <li><a href="./LocatorError.html">LocatorError</a></li>
-
- <li><a href="./OptionHandler.html">OptionHandler</a></li>
-
- <li><a href="./Read.html">Read</a></li>
-
- <li><a href="./SFF.html">SFF</a></li>
-
- <li><a href="./SFFError.html">SFFError</a></li>
-
- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
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- <div id="documentation">
- <h1 class="class">Locator</h1>
-
- <div id="description">
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
- <div id="attribute-method-details" class="method-section section">
- <h3 class="section-header">Attributes</h3>
-
-
- <div id="locator-attribute-method" class="method-detail">
- <a name="locator"></a>
-
- <a name="locator="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">locator</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="seq-attribute-method" class="method-detail">
- <a name="seq"></a>
-
- <a name="seq="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">seq</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="subseq-attribute-method" class="method-detail">
- <a name="subseq"></a>
-
- <a name="subseq="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">subseq</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- </div>
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(locator, seq)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 242</span>
-242: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">seq</span>)
-243: <span class="ruby-ivar">@locator</span> = <span class="ruby-identifier">locator</span>
-244: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
-245: <span class="ruby-ivar">@subseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-value str">""</span>, <span class="ruby-value str">"dna"</span>)
-246: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>)
-247: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="s-beg-method" class="method-detail ">
- <a name="method-i-s_beg"></a>
-
- <div class="method-heading">
-
- <span class="method-name">s_beg</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="s-beg-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 257</span>
-257: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">s_beg</span>
-258: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/(\d+)/</span>
-259: <span class="ruby-keyword kw">return</span> <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-260: <span class="ruby-keyword kw">end</span>
-261: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="s-end-method" class="method-detail ">
- <a name="method-i-s_end"></a>
-
- <div class="method-heading">
-
- <span class="method-name">s_end</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="s-end-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 263</span>
-263: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">s_end</span>
-264: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span>.<span class="ruby-identifier">reverse</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/(\d+)/</span>
-265: <span class="ruby-keyword kw">return</span> <span class="ruby-node">$1</span>.<span class="ruby-identifier">reverse</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-266: <span class="ruby-keyword kw">end</span>
-267: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="strand-method" class="method-detail ">
- <a name="method-i-strand"></a>
-
- <div class="method-heading">
-
- <span class="method-name">strand</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="strand-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 249</span>
-249: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">strand</span>
-250: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span>.<span class="ruby-identifier">match</span>(<span class="ruby-value str">"complement"</span>)
-251: <span class="ruby-keyword kw">return</span> <span class="ruby-value str">"-"</span>
-252: <span class="ruby-keyword kw">else</span>
-253: <span class="ruby-keyword kw">return</span> <span class="ruby-value str">"+"</span>
-254: <span class="ruby-keyword kw">end</span>
-255: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="balance-parens--method" class="method-detail ">
- <a name="method-i-balance_parens%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">balance_parens?</span><span
- class="method-args">(locator)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="balance-parens--source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 342</span>
-342: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">balance_parens?</span>(<span class="ruby-identifier">locator</span>)
-343: <span class="ruby-identifier">parens</span> = <span class="ruby-value">0</span>
-344:
-345: <span class="ruby-identifier">locator</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
-346: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">char</span>
-347: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'('</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-348: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">')'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
-349: <span class="ruby-keyword kw">end</span>
-350: <span class="ruby-keyword kw">end</span>
-351:
-352: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-353: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-354: <span class="ruby-keyword kw">else</span>
-355: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-356: <span class="ruby-keyword kw">end</span>
-357: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="parse-locator-method" class="method-detail ">
- <a name="method-i-parse_locator"></a>
-
- <div class="method-heading">
-
- <span class="method-name">parse_locator</span><span
- class="method-args">(locator, join = nil, comp = nil, order = nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that uses recursion to parse a locator string from a feature table
-and fetches the appropriate subsequence. the operators join(),
-complement(), and order() are handled. the locator string is broken into a
-comma separated lists, and modified if the parens donnot balance. otherwise
-the comma separated list of ranges are stripped from operators, and the
-subsequence are fetched and handled according to the operators. SNP
-locators are also dealt with (single positions).
-</p>
-
-
-
- <div class="method-source-code"
- id="parse-locator-source">
-<pre>
- <span class="ruby-comment cmt"># File genbank.rb, line 279</span>
-279: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">nil</span>)
-280: <span class="ruby-identifier">intervals</span> = <span class="ruby-identifier">locator</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">","</span>)
-281:
-282: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">balance_parens?</span>(<span class="ruby-identifier">intervals</span>.<span class="ruby-identifier">first</span>) <span class="ruby-comment cmt"># locator includes a join/comp/order of several ranges</span>
-283: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">locator</span>
-284: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^join\((.*)\)$/</span>
-285: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-286: <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">true</span>
-287: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^complement\((.*)\)$/</span>
-288: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-289: <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">true</span>
-290: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^order\((.*)\)$/</span>
-291: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-292: <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">true</span>
-293: <span class="ruby-keyword kw">end</span>
-294:
-295: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
-296: <span class="ruby-keyword kw">else</span>
-297: <span class="ruby-identifier">intervals</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">interval</span><span class="ruby-operator">|</span>
-298: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">interval</span>
-299: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^join\((.*)\)$/</span>
-300: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-301: <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">true</span>
-302: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
-303: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^complement\((.*)\)$/</span>
-304: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-305: <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">true</span>
-306: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
-307: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^order\((.*)\)$/</span>
-308: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
-309: <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">true</span>
-310: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
-311: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^[<>]?(\d+)[^\d]+(\d+)$/</span>
-312: <span class="ruby-identifier">int_beg</span> = <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-313: <span class="ruby-identifier">int_end</span> = <span class="ruby-node">$2</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-314:
-315: <span class="ruby-identifier">newseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">int_beg</span><span class="ruby-operator">...</span><span class="ruby-identifier">int_end</span>], <span class="ruby-value str">"dna"</span>)
-316:
-317: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-318: <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">revcomp</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">comp</span>
-319:
-320: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> (<span class="ruby-identifier">order</span> <span class="ruby-operator">?</span> <span class="ruby-value str">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>)
-321: <span class="ruby-keyword kw">end</span>
-322: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^(\d+)$/</span>
-323: <span class="ruby-identifier">pos</span> = <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-324:
-325: <span class="ruby-identifier">newseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span>], <span class="ruby-value str">"dna"</span>)
-326:
-327: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-328: <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">revcomp</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">comp</span>
-329:
-330: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> (<span class="ruby-identifier">order</span> <span class="ruby-operator">?</span> <span class="ruby-value str">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>)
-331: <span class="ruby-keyword kw">end</span>
-332: <span class="ruby-keyword kw">else</span>
-333: <span class="ruby-identifier">$stderr</span>.<span class="ruby-identifier">puts</span> <span class="ruby-node">"WARNING: Could not match locator -> #{locator}"</span>;
-334: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">""</span>
-335: <span class="ruby-keyword kw">end</span>
-336: <span class="ruby-keyword kw">end</span>
-337: <span class="ruby-keyword kw">end</span>
-338:
-339: <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@subseq</span>
-340: <span class="ruby-keyword kw">end</span></pre>
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-
- <li><a href="./LocatorError.html">LocatorError</a></li>
-
- <li><a href="./OptionHandler.html">OptionHandler</a></li>
-
- <li><a href="./Read.html">Read</a></li>
-
- <li><a href="./SFF.html">SFF</a></li>
-
- <li><a href="./SFFError.html">SFFError</a></li>
-
- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">OptionHandler</h1>
-
- <div id="description">
- <p>
-Class for parsing argv using OptionParser according to given casts. Default
-options are set, file glob expressions expanded, and options are checked
-according to the casts. Usage information is printed and exit called if
-required.
-</p>
-
- </div>
-
- <!-- Constants -->
-
- <div id="constants-list" class="section">
- <h3 class="section-header">Constants</h3>
- <dl>
-
- <dt><a name="REGEX_LIST">REGEX_LIST</a></dt>
-
- <dd class="description"></dd>
-
-
- <dt><a name="REGEX_INT">REGEX_INT</a></dt>
-
- <dd class="description"></dd>
-
-
- <dt><a name="REGEX_STRING">REGEX_STRING</a></dt>
-
- <dd class="description"></dd>
-
-
- </dl>
- </div>
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(argv, casts, script_path, test=nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 266</span>
-266: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>)
-267: <span class="ruby-ivar">@argv</span> = <span class="ruby-identifier">argv</span>
-268: <span class="ruby-ivar">@casts</span> = <span class="ruby-identifier">casts</span>
-269: <span class="ruby-ivar">@script_path</span> = <span class="ruby-identifier">script_path</span>
-270: <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
-271: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="options-check-method" class="method-detail ">
- <a name="method-i-options_check"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check all options according to casts.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 407</span>
-407: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check</span>
-408: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-409: <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
-410: <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
-411: <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
-412: <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
-413: <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
-414: <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
-415: <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
-416: <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
-417: <span class="ruby-keyword kw">end</span>
-418: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-allowed-method" class="method-detail ">
- <a name="method-i-options_check_allowed"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_allowed</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check options and raise unless allowed.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-allowed-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 470</span>
-470: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
-471: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-472: <span class="ruby-identifier">allowed_hash</span> = {}
-473: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">allowed_hash</span>[<span class="ruby-identifier">a</span>.<span class="ruby-identifier">to_s</span>] = <span class="ruby-value">1</span> }
-474:
-475: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">allowed_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">to_s</span>
-476: <span class="ruby-keyword kw">end</span>
-477: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-dir-method" class="method-detail ">
- <a name="method-i-options_check_dir"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_dir</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check dir! type argument and raise if directory don’t exist.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-dir-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 463</span>
-463: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
-464: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'dir!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-465: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such directory: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]]
-466: <span class="ruby-keyword kw">end</span>
-467: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-disallowed-method" class="method-detail ">
- <a name="method-i-options_check_disallowed"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_disallowed</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check disallowed argument values and raise if disallowed.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-disallowed-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 480</span>
-480: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
-481: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-482: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">val</span><span class="ruby-operator">|</span>
-483: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">to_s</span>
-484: <span class="ruby-keyword kw">end</span>
-485: <span class="ruby-keyword kw">end</span>
-486: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-file-method" class="method-detail ">
- <a name="method-i-options_check_file"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_file</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check file! type argument and raise if file don’t exists.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-file-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 446</span>
-446: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
-447: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'file!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-448: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such file: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]]
-449: <span class="ruby-keyword kw">end</span>
-450: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-files-method" class="method-detail ">
- <a name="method-i-options_check_files"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_files</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check files! type argument and raise if files don’t exists.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-files-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 453</span>
-453: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
-454: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-455: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
-456: <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">path</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
-457: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"File not readable: '#{path}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">readable?</span> <span class="ruby-identifier">path</span>
-458: <span class="ruby-keyword kw">end</span>
-459: <span class="ruby-keyword kw">end</span>
-460: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-int-method" class="method-detail ">
- <a name="method-i-options_check_int"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_int</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check int type option and raise if not an integer.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-int-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 428</span>
-428: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
-429: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'int'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-430: <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span>
-431: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"</span>
-432: <span class="ruby-keyword kw">end</span>
-433: <span class="ruby-keyword kw">end</span>
-434: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-mandatory-method" class="method-detail ">
- <a name="method-i-options_check_mandatory"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_mandatory</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if a mandatory option is set and raise if it isn’t.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-mandatory-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 421</span>
-421: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
-422: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>]
-423: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Mandatory argument: --#{cast[:long]}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-424: <span class="ruby-keyword kw">end</span>
-425: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-check-uint-method" class="method-detail ">
- <a name="method-i-options_check_uint"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_check_uint</span><span
- class="method-args">(cast)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check uint type option and raise if not an unsinged integer.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-check-uint-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 437</span>
-437: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
-438: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'uint'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-439: <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] <span class="ruby-operator">>=</span> <span class="ruby-value">0</span>
-440: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"</span>
-441: <span class="ruby-keyword kw">end</span>
-442: <span class="ruby-keyword kw">end</span>
-443: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-default-method" class="method-detail ">
- <a name="method-i-options_default"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_default</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Set default options value from cast unless a value is set.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-default-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 374</span>
-374: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_default</span>
-375: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-376: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>]
-377: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-378: <span class="ruby-keyword kw">end</span>
-379: <span class="ruby-keyword kw">end</span>
-380: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-glob-method" class="method-detail ">
- <a name="method-i-options_glob"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_glob</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Expands glob expressions to a full list of paths. Examples:
-“*.fna” or “foo.fna,*.fna” or
-“foo.fna,/bar/*.fna“
-</p>
-
-
-
- <div class="method-source-code"
- id="options-glob-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 384</span>
-384: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_glob</span>
-385: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-386: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files'</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span>
-387: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
-388: <span class="ruby-identifier">files</span> = []
-389:
-390: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
-391: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">path</span>.<span class="ruby-identifier">include?</span> <span class="ruby-value str">"*"</span>
-392: <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">glob</span>(<span class="ruby-identifier">path</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
-393: <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">file</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">file</span>
-394: <span class="ruby-keyword kw">end</span>
-395: <span class="ruby-keyword kw">else</span>
-396: <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">path</span>
-397: <span class="ruby-keyword kw">end</span>
-398: <span class="ruby-keyword kw">end</span>
-399:
-400: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">files</span>
-401: <span class="ruby-keyword kw">end</span>
-402: <span class="ruby-keyword kw">end</span>
-403: <span class="ruby-keyword kw">end</span>
-404: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="options-parse-method" class="method-detail ">
- <a name="method-i-options_parse"></a>
-
- <div class="method-heading">
-
- <span class="method-name">options_parse</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Parse options from argv using OptionParser and casts denoting long and
-short option names. Usage information is printed and exit called. A hash
-with options is returned.
-</p>
-
-
-
- <div class="method-source-code"
- id="options-parse-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 276</span>
-276: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_parse</span>
-277: <span class="ruby-ivar">@options</span> = {}
-278:
-279: <span class="ruby-identifier">option_parser</span> = <span class="ruby-constant">OptionParser</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">option</span><span class="ruby-operator">|</span>
-280: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
-281: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>]
-282: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'flag'</span>
-283: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]}"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">o</span><span class="ruby-operator">|</span>
-284: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">o</span>
-285: <span class="ruby-keyword kw">end</span>
-286: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'float'</span>
-287: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} F"</span>, <span class="ruby-constant">Float</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
-288: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">f</span>
-289: <span class="ruby-keyword kw">end</span>
-290: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'string'</span>
-291: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} S"</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
-292: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">s</span>.<span class="ruby-identifier">to_sym</span>
-293: <span class="ruby-keyword kw">end</span>
-294: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_LIST</span>
-295: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>( <span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} A"</span>, <span class="ruby-constant">Array</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
-296: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">a</span>
-297: <span class="ruby-keyword kw">end</span>
-298: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_INT</span>
-299: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} I"</span>, <span class="ruby-constant">Integer</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
-300: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">i</span>
-301: <span class="ruby-keyword kw">end</span>
-302: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_STRING</span>
-303: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} S"</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
-304: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">s</span>
-305: <span class="ruby-keyword kw">end</span>
-306: <span class="ruby-keyword kw">else</span>
-307: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Unknown option type: '#{cast[:type]}'"</span>
-308: <span class="ruby-keyword kw">end</span>
-309: <span class="ruby-keyword kw">end</span>
-310: <span class="ruby-keyword kw">end</span>
-311:
-312: <span class="ruby-identifier">option_parser</span>.<span class="ruby-identifier">parse!</span>(<span class="ruby-ivar">@argv</span>)
-313:
-314: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">print_usage_full?</span>
-315: <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-keyword kw">true</span>)
-316: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">print_usage_short?</span>
-317: <span class="ruby-identifier">print_usage_and_exit</span>
-318: <span class="ruby-keyword kw">end</span>
-319:
-320: <span class="ruby-identifier">options_default</span>
-321: <span class="ruby-identifier">options_glob</span>
-322: <span class="ruby-identifier">options_check</span>
-323:
-324: <span class="ruby-ivar">@options</span>
-325: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="print-usage-and-exit-method" class="method-detail ">
- <a name="method-i-print_usage_and_exit"></a>
-
- <div class="method-heading">
-
- <span class="method-name">print_usage_and_exit</span><span
- class="method-args">(full=nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Print usage info by Calling an external script ‘print_wiki’
-using a system() call and exit. An optional ‘full’ flag outputs
-the full usage info.
-</p>
-
-
-
- <div class="method-source-code"
- id="print-usage-and-exit-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 357</span>
-357: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-identifier">full</span>=<span class="ruby-keyword kw">nil</span>)
-358: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@test</span>
-359: <span class="ruby-keyword kw">return</span>
-360: <span class="ruby-keyword kw">else</span>
-361: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">full</span>
-362: <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path} --help"</span>)
-363: <span class="ruby-keyword kw">else</span>
-364: <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path}"</span>)
-365: <span class="ruby-keyword kw">end</span>
-366:
-367: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Failed printing wiki: #{wiki_path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">success?</span>
-368:
-369: <span class="ruby-identifier">exit</span>
-370: <span class="ruby-keyword kw">end</span>
-371: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="print-usage-full--method" class="method-detail ">
- <a name="method-i-print_usage_full%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">print_usage_full?</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if full “usage info” should be printed.
-</p>
-
-
-
- <div class="method-source-code"
- id="print-usage-full--source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 335</span>
-335: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_full?</span>
-336: <span class="ruby-ivar">@options</span>[<span class="ruby-value">:help</span>]
-337: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="print-usage-short--method" class="method-detail ">
- <a name="method-i-print_usage_short%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">print_usage_short?</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if short “usage info” should be printed.
-</p>
-
-
-
- <div class="method-source-code"
- id="print-usage-short--source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 340</span>
-340: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_short?</span>
-341: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span>
-342: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-343: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value">:stream_in</span>]
-344: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-345: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value">:data_in</span>]
-346: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-347: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">wiki_path</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/</span> <span class="ruby-comment cmt"># TODO get rid of this!</span>
-348: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
-349: <span class="ruby-keyword kw">else</span>
-350: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
-351: <span class="ruby-keyword kw">end</span>
-352: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="wiki-path-method" class="method-detail ">
- <a name="method-i-wiki_path"></a>
-
- <div class="method-heading">
-
- <span class="method-name">wiki_path</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Given the script name determine the path of the wiki file with the usage
-info.
-</p>
-
-
-
- <div class="method-source-code"
- id="wiki-path-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 328</span>
-328: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">wiki_path</span>
-329: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_DIR"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/bp_usage/"</span> <span class="ruby-operator">+</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-ivar">@script_path</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">".wiki"</span>
-330: <span class="ruby-identifier">raise</span> <span class="ruby-node">"No such wiki file: #{path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">path</span>
-331: <span class="ruby-identifier">path</span>
-332: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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-
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-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">Read</h1>
-
- <div id="description">
- <p>
-Class containing data accessor methods for an <a href="SFF.html">SFF</a>
-entry and methods for manipulating this entry.
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
- <div id="attribute-method-details" class="method-section section">
- <h3 class="section-header">Attributes</h3>
-
-
- <div id="read-header-length-attribute-method" class="method-detail">
- <a name="read_header_length"></a>
-
- <a name="read_header_length="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">read_header_length</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="name-length-attribute-method" class="method-detail">
- <a name="name_length"></a>
-
- <a name="name_length="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">name_length</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="number-of-bases-attribute-method" class="method-detail">
- <a name="number_of_bases"></a>
-
- <a name="number_of_bases="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">number_of_bases</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="clip-qual-left-attribute-method" class="method-detail">
- <a name="clip_qual_left"></a>
-
- <a name="clip_qual_left="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">clip_qual_left</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="clip-qual-right-attribute-method" class="method-detail">
- <a name="clip_qual_right"></a>
-
- <a name="clip_qual_right="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">clip_qual_right</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="clip-adapter-left-attribute-method" class="method-detail">
- <a name="clip_adapter_left"></a>
-
- <a name="clip_adapter_left="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">clip_adapter_left</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="clip-adaptor-right-attribute-method" class="method-detail">
- <a name="clip_adaptor_right"></a>
-
- <a name="clip_adaptor_right="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">clip_adaptor_right</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="name-attribute-method" class="method-detail">
- <a name="name"></a>
-
- <a name="name="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">name</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="flowgram-values-attribute-method" class="method-detail">
- <a name="flowgram_values"></a>
-
- <a name="flowgram_values="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">flowgram_values</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="flow-index-per-base-attribute-method" class="method-detail">
- <a name="flow_index_per_base"></a>
-
- <a name="flow_index_per_base="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">flow_index_per_base</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="bases-attribute-method" class="method-detail">
- <a name="bases"></a>
-
- <a name="bases="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">bases</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="quality-scores-attribute-method" class="method-detail">
- <a name="quality_scores"></a>
-
- <a name="quality_scores="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">quality_scores</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="x-pos-attribute-method" class="method-detail">
- <a name="x_pos"></a>
-
- <a name="x_pos="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">x_pos</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="y-pos-attribute-method" class="method-detail">
- <a name="y_pos"></a>
-
- <a name="y_pos="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">y_pos</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- </div>
-
-
- <!-- Methods -->
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="clip-method" class="method-detail ">
- <a name="method-i-clip"></a>
-
- <div class="method-heading">
-
- <span class="method-name">clip</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that clips sequence (i.e. trims) according to <a
-href="Read.html#clip_qual_left">clip_qual_left</a> and <a
-href="Read.html#clip_qual_right">clip_qual_right</a> information.
-</p>
-
-
-
- <div class="method-source-code"
- id="clip-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 228</span>
-228: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">clip</span>
-229: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
-230: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
-231: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="mask-method" class="method-detail ">
- <a name="method-i-mask"></a>
-
- <div class="method-heading">
-
- <span class="method-name">mask</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that soft masks the sequence (i.e. lowercases sequence) according to
-<a href="Read.html#clip_qual_left">clip_qual_left</a> and <a
-href="Read.html#clip_qual_right">clip_qual_right</a> information.
-</p>
-
-
-
- <div class="method-source-code"
- id="mask-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 218</span>
-218: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mask</span>
-219: <span class="ruby-identifier">left</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">downcase</span>
-220: <span class="ruby-identifier">middle</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
-221: <span class="ruby-identifier">right</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">downcase</span>
-222:
-223: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-identifier">left</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">middle</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">right</span>
-224: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-bp-method" class="method-detail ">
- <a name="method-i-to_bp"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_bp</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that converts a <a href="Read.html">Read</a> object’s data to
-a Biopiece record (a hash).
-</p>
-
-
-
- <div class="method-source-code"
- id="to-bp-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 197</span>
-197: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
-198: <span class="ruby-identifier">coordinates_get</span>
-199:
-200: <span class="ruby-identifier">hash</span> = {}
-201:
-202: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_NAME</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>
-203: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>
-204: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>
-205: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_LEFT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-206: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_RIGHT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-207: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_LEFT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adapter_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-208: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_RIGHT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adaptor_right</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-209: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SCORES</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> (<span class="ruby-identifier">i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">64</span>).<span class="ruby-identifier">chr</span> }.<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-210: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:X_POS</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span>
-211: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:Y_POS</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span>
-212:
-213: <span class="ruby-identifier">hash</span>
-214: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="coordinates-get-method" class="method-detail ">
- <a name="method-i-coordinates_get"></a>
-
- <div class="method-heading">
-
- <span class="method-name">coordinates_get</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that extracts the X/Y coordinates from an <a href="SFF.html">SFF</a>
-read name encoded with base36.
-</p>
-
-
-
- <div class="method-source-code"
- id="coordinates-get-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 237</span>
-237: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">coordinates_get</span>
-238: <span class="ruby-identifier">base36</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>[<span class="ruby-value">5</span>, <span class="ruby-value">5</span>]
-239: <span class="ruby-identifier">num</span> = <span class="ruby-constant">Base36</span>.<span class="ruby-identifier">decode</span>(<span class="ruby-identifier">base36</span>)
-240:
-241: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span> = <span class="ruby-identifier">num</span> <span class="ruby-operator">>></span> <span class="ruby-constant">BIT_SHIFT</span>
-242: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span> = <span class="ruby-identifier">num</span> & <span class="ruby-constant">BIT_MASK</span>
-243: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: SFF</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-
-</head>
-<body class="class">
-
- <div id="metadata">
- <div id="home-metadata">
- <div id="home-section" class="section">
- <h3 class="section-header">
- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
- </div>
- </div>
-
- <div id="file-metadata">
- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./sff_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="sff.rb">sff.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">Object</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
-
-
- <!-- Method Quickref -->
-
- <div id="method-list-section" class="section">
- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-new">::new</a></li>
-
- <li><a href="#method-c-open">::open</a></li>
-
- <li><a href="#method-i-check_header_length">#check_header_length</a></li>
-
- <li><a href="#method-i-check_magic_number">#check_magic_number</a></li>
-
- <li><a href="#method-i-check_version">#check_version</a></li>
-
- <li><a href="#method-i-close">#close</a></li>
-
- <li><a href="#method-i-each">#each</a></li>
-
- <li><a href="#method-i-fast_forward">#fast_forward</a></li>
-
- <li><a href="#method-i-header_parse">#header_parse</a></li>
-
- <li><a href="#method-i-read_parse">#read_parse</a></li>
-
- </ul>
- </div>
-
-
- <!-- Included Modules -->
-
- <div id="includes-section" class="section">
- <h3 class="section-header">Included Modules</h3>
- <ul class="link-list">
-
-
- <li><span class="include">Enumerable</span></li>
-
-
- </ul>
- </div>
-
- </div>
-
- <div id="project-metadata">
-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
- </form>
-
- <ul class="link-list">
-
- <li><a href="./Base36.html">Base36</a></li>
-
- <li><a href="./Base36Error.html">Base36Error</a></li>
-
- <li><a href="./Biopieces.html">Biopieces</a></li>
-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
- <li><a href="./CastError.html">CastError</a></li>
-
- <li><a href="./Casts.html">Casts</a></li>
-
- <li><a href="./Digest.html">Digest</a></li>
-
- <li><a href="./DigestError.html">DigestError</a></li>
-
- <li><a href="./Fasta.html">Fasta</a></li>
-
- <li><a href="./FastaError.html">FastaError</a></li>
-
- <li><a href="./Fastq.html">Fastq</a></li>
-
- <li><a href="./FastqError.html">FastqError</a></li>
-
- <li><a href="./Filesys.html">Filesys</a></li>
-
- <li><a href="./FilesysError.html">FilesysError</a></li>
-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
- <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
-
- <li><a href="./Locator.html">Locator</a></li>
-
- <li><a href="./LocatorError.html">LocatorError</a></li>
-
- <li><a href="./OptionHandler.html">OptionHandler</a></li>
-
- <li><a href="./Read.html">Read</a></li>
-
- <li><a href="./SFF.html">SFF</a></li>
-
- <li><a href="./SFFError.html">SFFError</a></li>
-
- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
-
- <li><a href="./StringError.html">StringError</a></li>
-
- </ul>
- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
- </div>
-
-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">SFF</h1>
-
- <div id="description">
- <p>
-Class containing methods to parse <a href="SFF.html">SFF</a> files: <a
-href="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff">www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff</a>
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(io)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to initialize an <a href="SFF.html">SFF</a> object along with
-instance variables pertaining to the <a href="SFF.html">SFF</a> header
-section.
-</p>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 58</span>
-58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>)
-59: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
-60: <span class="ruby-ivar">@magic_number</span> = <span class="ruby-value">0</span>
-61: <span class="ruby-ivar">@version</span> = <span class="ruby-value str">""</span>
-62: <span class="ruby-ivar">@index_offset</span> = <span class="ruby-value">0</span>
-63: <span class="ruby-ivar">@index_length</span> = <span class="ruby-value">0</span>
-64: <span class="ruby-ivar">@number_of_reads</span> = <span class="ruby-value">0</span>
-65: <span class="ruby-ivar">@header_length</span> = <span class="ruby-value">0</span>
-66: <span class="ruby-ivar">@key_length</span> = <span class="ruby-value">0</span>
-67: <span class="ruby-ivar">@number_of_flows_per_read</span> = <span class="ruby-value">0</span>
-68: <span class="ruby-ivar">@flowgram_format_code</span> = <span class="ruby-value">0</span>
-69: <span class="ruby-ivar">@flow_chars</span> = <span class="ruby-value str">""</span>
-70: <span class="ruby-ivar">@key_sequence</span> = <span class="ruby-value str">""</span>
-71: <span class="ruby-ivar">@eight_byte_padding</span> = <span class="ruby-value">0</span>
-72:
-73: <span class="ruby-identifier">header_parse</span>
-74: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="open-method" class="method-detail ">
- <a name="method-c-open"></a>
-
- <div class="method-heading">
-
- <span class="method-name">open</span><span
- class="method-args">(*args)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Class method for opening <a href="SFF.html">SFF</a> files.
-</p>
-
-
-
- <div class="method-source-code"
- id="open-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 41</span>
-41: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
-42: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
-43:
-44: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
-45: <span class="ruby-keyword kw">begin</span>
-46: <span class="ruby-keyword kw">yield</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
-47: <span class="ruby-keyword kw">ensure</span>
-48: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
-49: <span class="ruby-keyword kw">end</span>
-50: <span class="ruby-keyword kw">else</span>
-51: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
-52: <span class="ruby-keyword kw">end</span>
-53: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="close-method" class="method-detail ">
- <a name="method-i-close"></a>
-
- <div class="method-heading">
-
- <span class="method-name">close</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to close ios.
-</p>
-
-
-
- <div class="method-source-code"
- id="close-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 77</span>
-77: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
-78: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
-79: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="each-method" class="method-detail ">
- <a name="method-i-each"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to iterate over each <a href="SFF.html">SFF</a> entry.
-</p>
-
-
-
- <div class="method-source-code"
- id="each-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 82</span>
-82: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
-83: <span class="ruby-keyword kw">while</span> (<span class="ruby-identifier">read</span> = <span class="ruby-identifier">read_parse</span>) <span class="ruby-keyword kw">do</span>
-84: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">read</span>
-85: <span class="ruby-keyword kw">end</span>
-86:
-87: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
-88: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="check-header-length-method" class="method-detail ">
- <a name="method-i-check_header_length"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_header_length</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to check the header length of an <a href="SFF.html">SFF</a> file.
-Raises an error if the header length don’t match the file position
-after reading the header section.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-header-length-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 183</span>
-183: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_header_length</span>
-184: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-node">"Bad header length: #{header_length}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@header_length</span>
-185: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-magic-number-method" class="method-detail ">
- <a name="method-i-check_magic_number"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_magic_number</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to check the magic number of an <a href="SFF.html">SFF</a> file.
-Raises an error if the magic number don’t match.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-magic-number-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 170</span>
-170: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_magic_number</span>
-171: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-value str">"Badly formatted SFF file."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@magic_number</span> <span class="ruby-operator">==</span> <span class="ruby-value">779314790</span>
-172: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="check-version-method" class="method-detail ">
- <a name="method-i-check_version"></a>
-
- <div class="method-heading">
-
- <span class="method-name">check_version</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to check the version number of an <a href="SFF.html">SFF</a> file.
-Raises an error if the version don’t match.
-</p>
-
-
-
- <div class="method-source-code"
- id="check-version-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 176</span>
-176: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_version</span>
-177: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-node">"Wrong version: #{@version}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@version</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
-178: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="fast-forward-method" class="method-detail ">
- <a name="method-i-fast_forward"></a>
-
- <div class="method-heading">
-
- <span class="method-name">fast_forward</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that reads the eight_byte_padding field found at the end of the data
-section and fast forwards, i.e. move the file read pointer, so that the
-length of the section is divisible by 8.
-</p>
-
-
-
- <div class="method-source-code"
- id="fast-forward-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 122</span>
-122: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">fast_forward</span>
-123: <span class="ruby-identifier">eight_byte_padding</span> = <span class="ruby-value">8</span> <span class="ruby-operator">-</span> (<span class="ruby-ivar">@io</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">%</span> <span class="ruby-value">8</span>)
-124:
-125: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">eight_byte_padding</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">eight_byte_padding</span> <span class="ruby-operator">==</span> <span class="ruby-value">8</span>
-126: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="header-parse-method" class="method-detail ">
- <a name="method-i-header_parse"></a>
-
- <div class="method-heading">
-
- <span class="method-name">header_parse</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to parse the <a href="SFF.html">SFF</a> file’s header section
-and load the information into the instance variables.
-</p>
-
-
-
- <div class="method-source-code"
- id="header-parse-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 94</span>
- 94: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">header_parse</span>
- 95: <span class="ruby-identifier">template</span> = <span class="ruby-value str">"NC4N2NNnnnC"</span>
- 96: <span class="ruby-identifier">bits_in_uint</span> = <span class="ruby-value">32</span>
- 97:
- 98: <span class="ruby-identifier">data</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">31</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-identifier">template</span>)
- 99:
-100: <span class="ruby-ivar">@magic_number</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">0</span>]
-101: <span class="ruby-ivar">@version</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-value">4</span>].<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-102: <span class="ruby-ivar">@index_offset</span> = (<span class="ruby-identifier">data</span>[<span class="ruby-value">5</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">bits_in_uint</span>) <span class="ruby-operator">|</span> <span class="ruby-identifier">data</span>[<span class="ruby-value">6</span>]
-103: <span class="ruby-ivar">@index_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">7</span>]
-104: <span class="ruby-ivar">@number_of_reads</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">8</span>]
-105: <span class="ruby-ivar">@header_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">9</span>]
-106: <span class="ruby-ivar">@key_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">10</span>]
-107: <span class="ruby-ivar">@number_of_flows_per_read</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">11</span>]
-108: <span class="ruby-ivar">@flowgram_format_code</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">12</span>]
-109: <span class="ruby-ivar">@flow_chars</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-ivar">@number_of_flows_per_read</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-110: <span class="ruby-ivar">@key_sequence</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-ivar">@key_length</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-111:
-112: <span class="ruby-identifier">fast_forward</span>
-113:
-114: <span class="ruby-identifier">check_magic_number</span>
-115: <span class="ruby-identifier">check_version</span>
-116: <span class="ruby-identifier">check_header_length</span>
-117: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="read-parse-method" class="method-detail ">
- <a name="method-i-read_parse"></a>
-
- <div class="method-heading">
-
- <span class="method-name">read_parse</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to parse a read section of an <a href="SFF.html">SFF</a> file.
-</p>
-
-
-
- <div class="method-source-code"
- id="read-parse-source">
-<pre>
- <span class="ruby-comment cmt"># File sff.rb, line 129</span>
-129: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">read_parse</span>
-130: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@number_of_reads</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">@@count</span>
-131:
-132: <span class="ruby-identifier">template</span> = <span class="ruby-value str">"nnNnnnn"</span>
-133:
-134: <span class="ruby-identifier">read</span> = <span class="ruby-constant">Read</span>.<span class="ruby-identifier">new</span>()
-135:
-136: <span class="ruby-identifier">data</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">16</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-identifier">template</span>)
-137:
-138: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">read_header_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">0</span>]
-139: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">name_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">1</span>]
-140: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">2</span>]
-141: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_qual_left</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">3</span>]
-142: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_qual_right</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">4</span>]
-143: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_adapter_left</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">5</span>]
-144: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_adaptor_right</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">6</span>]
-145: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">name_length</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-146:
-147: <span class="ruby-identifier">fast_forward</span>
-148:
-149: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">2</span> * <span class="ruby-ivar">@number_of_flows_per_read</span>) <span class="ruby-comment cmt"># skip through flowgram_values</span>
-150: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>) <span class="ruby-comment cmt"># skip through flow_index_per_base</span>
-151:
-152: <span class="ruby-comment cmt"># NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.</span>
-153: <span class="ruby-comment cmt"># read.flowgram_values = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }</span>
-154: <span class="ruby-comment cmt"># flow_index_per_base = @io.read(read.number_of_bases).unpack("C*")</span>
-155: <span class="ruby-comment cmt"># (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }</span>
-156: <span class="ruby-comment cmt"># read.flow_index_per_base = flow_index_per_base</span>
-157:
-158: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
-159: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">quality_scores</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"C*"</span>)
-160:
-161: <span class="ruby-identifier">fast_forward</span>
-162:
-163: <span class="ruby-identifier">@@count</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-164:
-165: <span class="ruby-identifier">read</span>
-166: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
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- <li><a href="#method-c-generate_oligos">::generate_oligos</a></li>
-
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-
- <li><a href="#method-i-adaptor_clip_left">#adaptor_clip_left</a></li>
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-
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-
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-
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-
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-
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- <li><a href="#method-i-is_rna%3F">#is_rna?</a></li>
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-
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-
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-
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- <div id="seq-name-attribute-method" class="method-detail">
- <a name="seq_name"></a>
-
- <a name="seq_name="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">seq_name</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
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-
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- <a name="seq"></a>
-
- <a name="seq="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">seq</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
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-
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- </div>
- </div>
-
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- <a name="type"></a>
-
- <a name="type="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">type</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- <div id="qual-attribute-method" class="method-detail">
- <a name="qual"></a>
-
- <a name="qual="></a>
-
- <div class="method-heading attribute-method-heading">
- <span class="method-name">qual</span><span
- class="attribute-access-type">[RW]</span>
- </div>
-
- <div class="method-description">
-
-
-
- </div>
- </div>
-
- </div>
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="generate-oligos-method" class="method-detail ">
- <a name="method-c-generate_oligos"></a>
-
- <div class="method-heading">
-
- <span class="method-name">generate_oligos</span><span
- class="method-args">(length, type)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that generates all possible oligos of a specifed length and type.
-</p>
-
-
-
- <div class="method-source-code"
- id="generate-oligos-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 47</span>
-47: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">generate_oligos</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">type</span>)
-48: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative oligo length: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-49:
-50: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
-51: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/dna/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
-52: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/rna/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
-53: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/protein/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
-54: <span class="ruby-keyword kw">else</span>
-55: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
-56: <span class="ruby-keyword kw">end</span>
-57:
-58: <span class="ruby-identifier">oligos</span> = [<span class="ruby-value str">""</span>]
-59:
-60: (<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">length</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span>
-61: <span class="ruby-identifier">list</span> = []
-62:
-63: <span class="ruby-identifier">oligos</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">oligo</span><span class="ruby-operator">|</span>
-64: <span class="ruby-identifier">alph</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
-65: <span class="ruby-identifier">list</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">oligo</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">char</span>
-66: <span class="ruby-keyword kw">end</span>
-67: <span class="ruby-keyword kw">end</span>
-68:
-69: <span class="ruby-identifier">oligos</span> = <span class="ruby-identifier">list</span>
-70: <span class="ruby-keyword kw">end</span>
-71:
-72: <span class="ruby-identifier">oligos</span>
-73: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="new-method" class="method-detail ">
- <a name="method-c-new"></a>
-
- <div class="method-heading">
-
- <span class="method-name">new</span><span
- class="method-args">(seq_name = nil, seq = nil, type = nil, qual = nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize a sequence object with the following arguments:
-</p>
-<ul>
-<li><p>
-<a href="Seq.html#seq_name">seq_name</a>: Name of the sequence.
-</p>
-</li>
-<li><p>
-seq: The sequence.
-</p>
-</li>
-<li><p>
-type: The sequence type - DNA, RNA, or protein
-</p>
-</li>
-<li><p>
-qual: An Illumina type quality scores string.
-</p>
-</li>
-</ul>
-
-
-
- <div class="method-source-code"
- id="new-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 80</span>
-80: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">seq_name</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">type</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">nil</span>)
-81: <span class="ruby-ivar">@seq_name</span> = <span class="ruby-identifier">seq_name</span>
-82: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
-83: <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
-84: <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">qual</span>
-85: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="adaptor-clip-left-method" class="method-detail ">
- <a name="method-i-adaptor_clip_left"></a>
-
- <div class="method-heading">
-
- <span class="method-name">adaptor_clip_left</span><span
- class="method-args">(adaptor, hd_percent = 0)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that locates an adaptor or part thereof in the sequence of a <a
-href="Seq.html">Seq</a> object beginning from the left and removes the
-adaptor sequence if found. The hd_percent is used to calculate the maximum
-hamming distance allowed for all possible overlaps.
-</p>
-
-
-
- <div class="method-source-code"
- id="adaptor-clip-left-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 377</span>
-377: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_clip_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
-378: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">adaptor_locate_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span>)
-379:
-380: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
-381: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>]
-382: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">length</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
-383: <span class="ruby-keyword kw">end</span>
-384: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="adaptor-clip-right-method" class="method-detail ">
- <a name="method-i-adaptor_clip_right"></a>
-
- <div class="method-heading">
-
- <span class="method-name">adaptor_clip_right</span><span
- class="method-args">(adaptor, hd_percent = 0)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that locates an adaptor or part thereof in the sequence of a <a
-href="Seq.html">Seq</a> object beginning from the right and removes the
-adaptor sequence if found. The hd_percent is used to calculate the maximum
-hamming distance allowed for all possible overlaps.
-</p>
-
-
-
- <div class="method-source-code"
- id="adaptor-clip-right-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 364</span>
-364: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_clip_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
-365: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">adaptor_locate_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span>)
-366:
-367: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
-368: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span>]
-369: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
-370: <span class="ruby-keyword kw">end</span>
-371: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="adaptor-locate-left-method" class="method-detail ">
- <a name="method-i-adaptor_locate_left"></a>
-
- <div class="method-heading">
-
- <span class="method-name">adaptor_locate_left</span><span
- class="method-args">(adaptor, hd_percent = 0)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that locates an adaptor or part thereof in the sequence of a <a
-href="Seq.html">Seq</a> object beginning from the left. Returns the
-location in the sequence that overlaps with the adaptor or -1 if the
-adaptor was not found. The hd_percent is used to calculate the maximum
-hamming distance allowed for all possible overlaps.
-</p>
-
-
-
- <div class="method-source-code"
- id="adaptor-locate-left-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 340</span>
-340: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_locate_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
-341: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Hamming distance percent out of range #{hd_percent}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">100</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">hd_percent</span>
-342: <span class="ruby-identifier">pos</span> = <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>
-343:
-344: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
-345: <span class="ruby-identifier">len</span> = <span class="ruby-identifier">pos</span>
-346: <span class="ruby-identifier">subseq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
-347: <span class="ruby-identifier">subadaptor</span> = <span class="ruby-identifier">adaptor</span>[<span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">len</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">upcase</span>
-348: <span class="ruby-identifier">m</span> = <span class="ruby-constant">Hamming</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">subseq</span>)
-349: <span class="ruby-identifier">hamming_dist</span> = <span class="ruby-identifier">m</span>.<span class="ruby-identifier">match</span>(<span class="ruby-identifier">subadaptor</span>)
-350: <span class="ruby-identifier">hamming_max</span> = (<span class="ruby-identifier">len</span> * <span class="ruby-identifier">hd_percent</span> * <span class="ruby-value">0.01</span>).<span class="ruby-identifier">round</span>
-351:
-352: <span class="ruby-identifier">pos</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
-353:
-354: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">pos</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hamming_dist</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">hamming_max</span>
-355: <span class="ruby-keyword kw">end</span>
-356:
-357: <span class="ruby-value">1</span>
-358: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="adaptor-locate-right-method" class="method-detail ">
- <a name="method-i-adaptor_locate_right"></a>
-
- <div class="method-heading">
-
- <span class="method-name">adaptor_locate_right</span><span
- class="method-args">(adaptor, hd_percent = 0)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that locates an adaptor or part thereof in the sequence of a <a
-href="Seq.html">Seq</a> object beginning from the right. Returns the
-location in the sequence that overlaps with the adaptor or -1 if the
-adaptor was not found. The hd_percent is used to calculate the maximum
-hamming distance allowed for all possible overlaps.
-</p>
-
-
-
- <div class="method-source-code"
- id="adaptor-locate-right-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 316</span>
-316: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_locate_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
-317: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Hamming distance percent out of range #{hd_percent}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">100</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">hd_percent</span>
-318: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>
-319:
-320: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator"><</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
-321: <span class="ruby-identifier">len</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">pos</span>
-322: <span class="ruby-identifier">subseq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
-323: <span class="ruby-identifier">subadaptor</span> = <span class="ruby-identifier">adaptor</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
-324: <span class="ruby-identifier">m</span> = <span class="ruby-constant">Hamming</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">subseq</span>)
-325: <span class="ruby-identifier">hamming_dist</span> = <span class="ruby-identifier">m</span>.<span class="ruby-identifier">match</span>(<span class="ruby-identifier">subadaptor</span>)
-326: <span class="ruby-identifier">hamming_max</span> = (<span class="ruby-identifier">len</span> * <span class="ruby-identifier">hd_percent</span> * <span class="ruby-value">0.01</span>).<span class="ruby-identifier">round</span>
-327: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">pos</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hamming_dist</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">hamming_max</span>
-328:
-329: <span class="ruby-identifier">pos</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-330: <span class="ruby-keyword kw">end</span>
-331:
-332: <span class="ruby-value">1</span>
-333: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="complement-method" class="method-detail ">
- <a name="method-i-complement"></a>
-
- <div class="method-heading">
-
- <span class="method-name">complement</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that complements sequence including ambiguity codes.
-</p>
-
-
-
- <div class="method-source-code"
- id="complement-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 196</span>
-196: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
-197: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot complement 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-198:
-199: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna?</span>
-200: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
-201: <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna?</span>
-202: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
-203: <span class="ruby-keyword kw">else</span>
-204: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
-205: <span class="ruby-keyword kw">end</span>
-206: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="composition-method" class="method-detail ">
- <a name="method-i-composition"></a>
-
- <div class="method-heading">
-
- <span class="method-name">composition</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the residue compositions of a sequence in a hash where
-the key is the residue and the value is the residue count.
-</p>
-
-
-
- <div class="method-source-code"
- id="composition-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 272</span>
-272: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">composition</span>
-273: <span class="ruby-identifier">comp</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>);
-274:
-275: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
-276: <span class="ruby-identifier">comp</span>[<span class="ruby-identifier">char</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
-277: <span class="ruby-keyword kw">end</span>
-278:
-279: <span class="ruby-identifier">comp</span>
-280: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="convert-phred-illumina--method" class="method-detail ">
- <a name="method-i-convert_phred2illumina%21"></a>
-
- <div class="method-heading">
-
- <span class="method-name">convert_phred2illumina!</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to convert the quality scores from a specified base to another base.
-</p>
-
-
-
- <div class="method-source-code"
- id="convert-phred-illumina--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 388</span>
-388: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">convert_phred2illumina!</span>
-389: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-regexp re">/./</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">score</span><span class="ruby-operator">|</span>
-390: <span class="ruby-identifier">score_phred</span> = <span class="ruby-identifier">score</span>.<span class="ruby-identifier">ord</span> <span class="ruby-operator">-</span> <span class="ruby-constant">SCORE_PHRED</span>
-391: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Bad Phred score: #{score} (#{score_phred})"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">40</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">score_phred</span>
-392: <span class="ruby-identifier">score_illumina</span> = <span class="ruby-identifier">score_phred</span> <span class="ruby-operator">+</span> <span class="ruby-constant">SCORE_ILLUMINA</span>
-393: <span class="ruby-identifier">score</span> = <span class="ruby-identifier">score_illumina</span>.<span class="ruby-identifier">chr</span>
-394: <span class="ruby-keyword kw">end</span>
-395: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="convert-solexa-illumina--method" class="method-detail ">
- <a name="method-i-convert_solexa2illumina%21"></a>
-
- <div class="method-heading">
-
- <span class="method-name">convert_solexa2illumina!</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to convert the quality scores from Solexa odd/ratio to Illumina
-format.
-</p>
-
-
-
- <div class="method-source-code"
- id="convert-solexa-illumina--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 399</span>
-399: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">convert_solexa2illumina!</span>
-400: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-regexp re">/./</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">score</span><span class="ruby-operator">|</span>
-401: <span class="ruby-identifier">score</span> = <span class="ruby-identifier">solexa_char2illumina_char</span>(<span class="ruby-identifier">score</span>)
-402: <span class="ruby-keyword kw">end</span>
-403: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="generate-method" class="method-detail ">
- <a name="method-i-generate"></a>
-
- <div class="method-heading">
-
- <span class="method-name">generate</span><span
- class="method-args">(length, type)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that generates a random sequence of a given length and type.
-</p>
-
-
-
- <div class="method-source-code"
- id="generate-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 209</span>
-209: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">type</span>)
-210: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate sequence length < 1: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-211:
-212: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
-213: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
-214: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
-215: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
-216: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
-217: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
-218: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
-219: <span class="ruby-keyword kw">else</span>
-220: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
-221: <span class="ruby-keyword kw">end</span>
-222:
-223: <span class="ruby-identifier">seq_new</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">length</span>) { <span class="ruby-identifier">alph</span>[<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span>)] }.<span class="ruby-identifier">join</span>(<span class="ruby-value str">""</span>)
-224: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
-225: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
-226: <span class="ruby-identifier">seq_new</span>
-227: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="hard-mask-method" class="method-detail ">
- <a name="method-i-hard_mask"></a>
-
- <div class="method-heading">
-
- <span class="method-name">hard_mask</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the percentage of hard masked residues or N’s in
-a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="hard-mask-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 301</span>
-301: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">hard_mask</span>
-302: ((<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-value str">"N"</span>).<span class="ruby-identifier">size</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">len</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">indels</span>).<span class="ruby-identifier">to_f</span>) * <span class="ruby-value">100</span>).<span class="ruby-identifier">round</span>(<span class="ruby-value">2</span>)
-303: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="homopol-max-method" class="method-detail ">
- <a name="method-i-homopol_max"></a>
-
- <div class="method-heading">
-
- <span class="method-name">homopol_max</span><span
- class="method-args">(min = 1)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the length of the longest homopolymeric stretch found
-in a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="homopol-max-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 284</span>
-284: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">homopol_max</span>(<span class="ruby-identifier">min</span> = <span class="ruby-value">1</span>)
-285: <span class="ruby-keyword kw">return</span> <span class="ruby-value">0</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">empty?</span>
-286:
-287: <span class="ruby-identifier">found</span> = <span class="ruby-keyword kw">false</span>
-288:
-289: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-node">/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">match</span><span class="ruby-operator">|</span>
-290: <span class="ruby-identifier">found</span> = <span class="ruby-keyword kw">true</span>
-291: <span class="ruby-identifier">min</span> = <span class="ruby-identifier">match</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">></span> <span class="ruby-identifier">min</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">match</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">min</span>
-292: <span class="ruby-keyword kw">end</span>
-293:
-294: <span class="ruby-keyword kw">return</span> <span class="ruby-value">0</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">found</span>
-295:
-296: <span class="ruby-identifier">min</span>
-297: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="indels-method" class="method-detail ">
- <a name="method-i-indels"></a>
-
- <div class="method-heading">
-
- <span class="method-name">indels</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Return the number indels in a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="indels-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 95</span>
-95: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">indels</span>
-96: <span class="ruby-identifier">regex</span> = <span class="ruby-constant">Regexp</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">/[#{Regexp.escape(INDELS.join(""))}]/</span>)
-97: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-identifier">regex</span>).<span class="ruby-identifier">size</span>
-98: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="is-dna--method" class="method-detail ">
- <a name="method-i-is_dna%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">is_dna?</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns true is a given sequence type is DNA.
-</p>
-
-
-
- <div class="method-source-code"
- id="is-dna--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 101</span>
-101: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna?</span>
-102: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'dna'</span>
-103: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="is-protein--method" class="method-detail ">
- <a name="method-i-is_protein%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">is_protein?</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns true is a given sequence type is protein.
-</p>
-
-
-
- <div class="method-source-code"
- id="is-protein--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 111</span>
-111: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein?</span>
-112: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'protein'</span>
-113: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="is-rna--method" class="method-detail ">
- <a name="method-i-is_rna%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">is_rna?</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns true is a given sequence type is RNA.
-</p>
-
-
-
- <div class="method-source-code"
- id="is-rna--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 106</span>
-106: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna?</span>
-107: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'rna'</span>
-108: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="len-method" class="method-detail method-alias">
- <a name="method-i-len"></a>
-
- <div class="method-heading">
-
- <span class="method-name">len</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- </div>
-
-
-
-
- <div class="aliases">
- Alias for: <a href="Seq.html#method-i-length">length</a>
- </div>
-
- </div>
-
-
- <div id="length-method" class="method-detail ">
- <a name="method-i-length"></a>
-
- <div class="method-heading">
-
- <span class="method-name">length</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Returns the length of a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="length-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 88</span>
-88: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">length</span>
-89: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">?</span> <span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">length</span>
-90: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
- <div class="aliases">
- Also aliased as: <a href="Seq.html#method-i-len">len</a>
- </div>
-
-
-
- </div>
-
-
- <div id="match-method" class="method-detail ">
- <a name="method-i-match"></a>
-
- <div class="method-heading">
-
- <span class="method-name">match</span><span
- class="method-args">(patter, pos)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <hr style="height: 10px"></hr><pre>
- seq.match(pattern[, pos ] [, hd=max] [, ed=max]) -> matchdata or nil
-</pre>
-<hr style="height: 10px"></hr><p>
-Method to locate a pattern in a sequence and return the position of the
-match or nil if no match was found. Optional maximum Hamming and Edit
-distance can be specified.
-</p>
-
-
-
- <div class="method-source-code"
- id="match-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 411</span>
-411: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match</span>(<span class="ruby-identifier">patter</span>, <span class="ruby-identifier">pos</span>)
-412: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="revcomp-method" class="method-detail method-alias">
- <a name="method-i-revcomp"></a>
-
- <div class="method-heading">
-
- <span class="method-name">revcomp</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
-
-
-
-
- </div>
-
-
-
-
- <div class="aliases">
- Alias for: <a href="Seq.html#method-i-reverse_complement">reverse_complement</a>
- </div>
-
- </div>
-
-
- <div id="reverse-method" class="method-detail ">
- <a name="method-i-reverse"></a>
-
- <div class="method-heading">
-
- <span class="method-name">reverse</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to reverse the sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="reverse-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 191</span>
-191: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">reverse</span>
-192: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">reverse!</span>
-193: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="reverse-complement-method" class="method-detail ">
- <a name="method-i-reverse_complement"></a>
-
- <div class="method-heading">
-
- <span class="method-name">reverse_complement</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to reverse complement sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="reverse-complement-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 183</span>
-183: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">reverse_complement</span>
-184: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">reverse</span>
-185: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">complement</span>
-186: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
- <div class="aliases">
- Also aliased as: <a href="Seq.html#method-i-revcomp">revcomp</a>
- </div>
-
-
-
- </div>
-
-
- <div id="soft-mask-method" class="method-detail ">
- <a name="method-i-soft_mask"></a>
-
- <div class="method-heading">
-
- <span class="method-name">soft_mask</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns the percentage of soft masked residues or lower cased
-residues in a sequence.
-</p>
-
-
-
- <div class="method-source-code"
- id="soft-mask-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 307</span>
-307: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">soft_mask</span>
-308: ((<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-regexp re">/[a-z]/</span>).<span class="ruby-identifier">size</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">len</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">indels</span>).<span class="ruby-identifier">to_f</span>) * <span class="ruby-value">100</span>).<span class="ruby-identifier">round</span>(<span class="ruby-value">2</span>)
-309: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="subseq-method" class="method-detail ">
- <a name="method-i-subseq"></a>
-
- <div class="method-heading">
-
- <span class="method-name">subseq</span><span
- class="method-args">(start, length = self.length - start)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns a subsequence of from a given start position and of a
-given length.
-</p>
-
-
-
- <div class="method-source-code"
- id="subseq-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 231</span>
-231: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">start</span>)
-232: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start: #{start} < 0"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
-233: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence length: #{length} < 1"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-234: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
-235:
-236: <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-237:
-238: <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>]
-239: <span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
-240:
-241: <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span>, <span class="ruby-identifier">qual</span>)
-242: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="subseq--method" class="method-detail ">
- <a name="method-i-subseq%21"></a>
-
- <div class="method-heading">
-
- <span class="method-name">subseq!</span><span
- class="method-args">(start, length = self.length - start)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that replaces a sequence with a subsequence from a given start
-position and of a given length.
-</p>
-
-
-
- <div class="method-source-code"
- id="subseq--source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 246</span>
-246: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq!</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">start</span>)
-247: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start: #{start} < 0"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
-248: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence length: #{length} < 1"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-249: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
-250:
-251: <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
-252:
-253: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>]
-254: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
-255: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="subseq-rand-method" class="method-detail ">
- <a name="method-i-subseq_rand"></a>
-
- <div class="method-heading">
-
- <span class="method-name">subseq_rand</span><span
- class="method-args">(length)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns a subsequence of a given length beginning at a random
-position.
-</p>
-
-
-
- <div class="method-source-code"
- id="subseq-rand-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 259</span>
-259: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq_rand</span>(<span class="ruby-identifier">length</span>)
-260: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-261: <span class="ruby-identifier">start</span> = <span class="ruby-value">0</span>
-262: <span class="ruby-keyword kw">else</span>
-263: <span class="ruby-identifier">start</span> = <span class="ruby-identifier">rand</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
-264: <span class="ruby-keyword kw">end</span>
-265:
-266: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">subseq</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span>)
-267: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-bp-method" class="method-detail ">
- <a name="method-i-to_bp"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_bp</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that given a <a href="Seq.html">Seq</a> entry returns a <a
-href="Biopieces.html">Biopieces</a> record (a hash).
-</p>
-
-
-
- <div class="method-source-code"
- id="to-bp-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 132</span>
-132: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
-133: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq_name"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span>
-134: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-135: <span class="ruby-identifier">record</span> = {}
-136: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_NAME</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
-137: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
-138: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
-139: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SCORES</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>
-140: <span class="ruby-identifier">record</span>
-141: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-dna-method" class="method-detail ">
- <a name="method-i-to_dna"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_dna</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to reverse-transcribe RNA to DNA.
-</p>
-
-
-
- <div class="method-source-code"
- id="to-dna-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 124</span>
-124: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
-125: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot reverse-transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-126: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot reverse-transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna?</span>
-127: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
-128: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Uu'</span>,<span class="ruby-value str">'Tt'</span>)
-129: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-fasta-method" class="method-detail ">
- <a name="method-i-to_fasta"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_fasta</span><span
- class="method-args">(wrap = nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that given a <a href="Seq.html">Seq</a> entry returns a FASTA entry
-(a string).
-</p>
-
-
-
- <div class="method-source-code"
- id="to-fasta-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 144</span>
-144: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_fasta</span>(<span class="ruby-identifier">wrap</span> = <span class="ruby-keyword kw">nil</span>)
-145: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq_name"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span>
-146: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-147:
-148: <span class="ruby-identifier">seq_name</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
-149: <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
-150:
-151: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">wrap</span>.<span class="ruby-identifier">nil?</span>
-152: <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-node">/(.{#{wrap}})/</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">match</span><span class="ruby-operator">|</span>
-153: <span class="ruby-identifier">match</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"\n"</span>
-154: <span class="ruby-keyword kw">end</span>
-155:
-156: <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">chomp!</span>
-157: <span class="ruby-keyword kw">end</span>
-158:
-159: <span class="ruby-node">">#{seq_name}\n#{seq}\n"</span>
-160: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-key-method" class="method-detail ">
- <a name="method-i-to_key"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_key</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that generates a unique key for a DNA sequence and return this key
-as a Fixnum.
-</p>
-
-
-
- <div class="method-source-code"
- id="to-key-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 164</span>
-164: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_key</span>
-165: <span class="ruby-identifier">key</span> = <span class="ruby-value">0</span>
-166:
-167: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
-168: <span class="ruby-identifier">key</span> <span class="ruby-operator"><<=</span> <span class="ruby-value">2</span>
-169:
-170: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">char</span>
-171: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'A'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">0</span>
-172: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'C'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">1</span>
-173: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'G'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">2</span>
-174: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'T'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">3</span>
-175: <span class="ruby-keyword kw">else</span> <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Bad residue: #{char}"</span>
-176: <span class="ruby-keyword kw">end</span>
-177: <span class="ruby-keyword kw">end</span>
-178:
-179: <span class="ruby-identifier">key</span>
-180: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="to-rna-method" class="method-detail ">
- <a name="method-i-to_rna"></a>
-
- <div class="method-heading">
-
- <span class="method-name">to_rna</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to transcribe DNA to RNA.
-</p>
-
-
-
- <div class="method-source-code"
- id="to-rna-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 116</span>
-116: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
-117: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-118: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna?</span>
-119: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
-120: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Tt'</span>,<span class="ruby-value str">'Uu'</span>)
-121: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="solexa-phred-method" class="method-detail ">
- <a name="method-i-solexa2phred"></a>
-
- <div class="method-heading">
-
- <span class="method-name">solexa2phred</span><span
- class="method-args">(score)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to convert a Solexa score (odd ratio) to a phred (probability)
-integer score.
-</p>
-
-
-
- <div class="method-source-code"
- id="solexa-phred-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 418</span>
-418: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">solexa2phred</span>(<span class="ruby-identifier">score</span>)
-419: (<span class="ruby-value">10.0</span> * <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-value">10.0</span> <span class="ruby-operator">**</span> (<span class="ruby-identifier">score</span> <span class="ruby-operator">/</span> <span class="ruby-value">10.0</span>) <span class="ruby-operator">+</span> <span class="ruby-value">1.0</span>, <span class="ruby-value">10</span>)).<span class="ruby-identifier">to_i</span>
-420: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="solexa-char-illumina-char-method" class="method-detail ">
- <a name="method-i-solexa_char2illumina_char"></a>
-
- <div class="method-heading">
-
- <span class="method-name">solexa_char2illumina_char</span><span
- class="method-args">(char)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to convert a Solexa score encoded using base 64 ASCII to a Phred
-score encoded using base 64 ASCII.
-</p>
-
-
-
- <div class="method-source-code"
- id="solexa-char-illumina-char-source">
-<pre>
- <span class="ruby-comment cmt"># File seq.rb, line 424</span>
-424: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">solexa_char2illumina_char</span>(<span class="ruby-identifier">char</span>)
-425: <span class="ruby-identifier">score_solexa</span> = <span class="ruby-identifier">char</span>.<span class="ruby-identifier">ord</span> <span class="ruby-operator">-</span> <span class="ruby-value">64</span>
-426: <span class="ruby-identifier">score_phred</span> = <span class="ruby-identifier">solexa2phred</span>(<span class="ruby-identifier">score_solexa</span>)
-427: (<span class="ruby-identifier">score_phred</span> <span class="ruby-operator">+</span> <span class="ruby-value">64</span>).<span class="ruby-identifier">chr</span>
-428: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: SeqError</title>
-
- <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-
-</head>
-<body class="class">
-
- <div id="metadata">
- <div id="home-metadata">
- <div id="home-section" class="section">
- <h3 class="section-header">
- <a href="./index.html">Home</a>
- <a href="./index.html#classes">Classes</a>
- <a href="./index.html#methods">Methods</a>
- </h3>
- </div>
- </div>
-
- <div id="file-metadata">
- <div id="file-list-section" class="section">
- <h3 class="section-header">In Files</h3>
- <div class="section-body">
- <ul>
-
- <li><a href="./seq_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="seq.rb">seq.rb</a></li>
-
- </ul>
- </div>
- </div>
-
-
- </div>
-
- <div id="class-metadata">
-
- <!-- Parent Class -->
-
- <div id="parent-class-section" class="section">
- <h3 class="section-header">Parent</h3>
-
- <p class="link">StandardError</p>
-
- </div>
-
-
- <!-- Namespace Contents -->
-
-
- <!-- Method Quickref -->
-
-
- <!-- Included Modules -->
-
- </div>
-
- <div id="project-metadata">
-
-
-
- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
- <input type="text" name="quicksearch" value=""
- class="quicksearch-field" />
- </fieldset>
- </form>
-
- <ul class="link-list">
-
- <li><a href="./Base36.html">Base36</a></li>
-
- <li><a href="./Base36Error.html">Base36Error</a></li>
-
- <li><a href="./Biopieces.html">Biopieces</a></li>
-
- <li><a href="./BitArray.html">BitArray</a></li>
-
- <li><a href="./BitArrayError.html">BitArrayError</a></li>
-
- <li><a href="./Boulder.html">Boulder</a></li>
-
- <li><a href="./BoulderError.html">BoulderError</a></li>
-
- <li><a href="./CastError.html">CastError</a></li>
-
- <li><a href="./Casts.html">Casts</a></li>
-
- <li><a href="./Digest.html">Digest</a></li>
-
- <li><a href="./DigestError.html">DigestError</a></li>
-
- <li><a href="./Fasta.html">Fasta</a></li>
-
- <li><a href="./FastaError.html">FastaError</a></li>
-
- <li><a href="./Fastq.html">Fastq</a></li>
-
- <li><a href="./FastqError.html">FastqError</a></li>
-
- <li><a href="./Filesys.html">Filesys</a></li>
-
- <li><a href="./FilesysError.html">FilesysError</a></li>
-
- <li><a href="./Genbank.html">Genbank</a></li>
-
- <li><a href="./GenbankError.html">GenbankError</a></li>
-
- <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
-
- <li><a href="./Locator.html">Locator</a></li>
-
- <li><a href="./LocatorError.html">LocatorError</a></li>
-
- <li><a href="./OptionHandler.html">OptionHandler</a></li>
-
- <li><a href="./Read.html">Read</a></li>
-
- <li><a href="./SFF.html">SFF</a></li>
-
- <li><a href="./SFFError.html">SFFError</a></li>
-
- <li><a href="./Seq.html">Seq</a></li>
-
- <li><a href="./SeqError.html">SeqError</a></li>
-
- <li><a href="./Status.html">Status</a></li>
-
- <li><a href="./Stream.html">Stream</a></li>
-
- <li><a href="./String.html">String</a></li>
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- <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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-
- </div>
- </div>
-
- <div id="documentation">
- <h1 class="class">SeqError</h1>
-
- <div id="description">
- <p>
-Error class for all exceptions to do with <a href="Seq.html">Seq</a>.
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
-
- </div>
-
-
- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
-
- </div>
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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- Rdoc Generator</a> 1.1.6</small>.</p>
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-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>Class: Status</title>
-
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- <h1 class="class">Status</h1>
-
- <div id="description">
- <p>
-Class for manipulating the execution status of <a
-href="Biopieces.html">Biopieces</a> by setting a status file with a time
-stamp, process id, and command arguments. The status file is used for
-creating log entries and for displaying the runtime status of <a
-href="Biopieces.html">Biopieces</a>.
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="delete-method" class="method-detail ">
- <a name="method-i-delete"></a>
-
- <div class="method-heading">
-
- <span class="method-name">delete</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Delete status file.
-</p>
-
-
-
- <div class="method-source-code"
- id="delete-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 547</span>
-547: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">delete</span>
-548: <span class="ruby-constant">File</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">path</span>)
-549: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="get-tmpdir-method" class="method-detail ">
- <a name="method-i-get_tmpdir"></a>
-
- <div class="method-heading">
-
- <span class="method-name">get_tmpdir</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Extract the temporary directory path from the status file, and return this
-or nil if not found.
-</p>
-
-
-
- <div class="method-source-code"
- id="get-tmpdir-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 520</span>
-520: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_tmpdir</span>
-521: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
-522: <span class="ruby-identifier">tmpdir_path</span> = <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>).<span class="ruby-identifier">last</span>
-523: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">tmpdir_path</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span>(<span class="ruby-identifier">tmpdir_path</span>)
-524: <span class="ruby-keyword kw">end</span>
-525:
-526: <span class="ruby-keyword kw">nil</span>
-527: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="log-method" class="method-detail ">
- <a name="method-i-log"></a>
-
- <div class="method-heading">
-
- <span class="method-name">log</span><span
- class="method-args">(exit_status)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Write the Biopiece status to the log file.
-</p>
-
-
-
- <div class="method-source-code"
- id="log-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 530</span>
-530: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">log</span>(<span class="ruby-identifier">exit_status</span>)
-531: <span class="ruby-identifier">time1</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
-532: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
-533: <span class="ruby-identifier">script</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-identifier">$0</span>)
-534:
-535: <span class="ruby-identifier">stream</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>)
-536: <span class="ruby-identifier">time0</span>, <span class="ruby-identifier">args</span>, <span class="ruby-identifier">tmp_dir</span> = <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>)
-537: <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">close</span>
-538:
-539: <span class="ruby-identifier">elap</span> = <span class="ruby-identifier">time_diff</span>(<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>)
-540: <span class="ruby-identifier">command</span> = [<span class="ruby-identifier">script</span>, <span class="ruby-identifier">args</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)
-541: <span class="ruby-identifier">log_file</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_LOG"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/biopieces.log"</span>
-542:
-543: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">log_file</span>, <span class="ruby-identifier">mode</span> = <span class="ruby-value str">"a"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span> <span class="ruby-identifier">file</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>, <span class="ruby-identifier">elap</span>, <span class="ruby-identifier">user</span>, <span class="ruby-identifier">exit_status</span>, <span class="ruby-identifier">command</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\t"</span>) }
-544: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="set-method" class="method-detail ">
- <a name="method-i-set"></a>
-
- <div class="method-heading">
-
- <span class="method-name">set</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Write the status to a status file.
-</p>
-
-
-
- <div class="method-source-code"
- id="set-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 495</span>
-495: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set</span>
-496: <span class="ruby-identifier">time0</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
-497:
-498: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
-499: <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-constant">ARGV</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)].<span class="ruby-identifier">join</span>(<span class="ruby-value str">";"</span>)
-500: <span class="ruby-keyword kw">end</span>
-501: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="set-tmpdir-method" class="method-detail ">
- <a name="method-i-set_tmpdir"></a>
-
- <div class="method-heading">
-
- <span class="method-name">set_tmpdir</span><span
- class="method-args">(tmpdir_path)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Append the a temporary directory path to the status file.
-</p>
-
-
-
- <div class="method-source-code"
- id="set-tmpdir-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 504</span>
-504: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">tmpdir_path</span>)
-505: <span class="ruby-identifier">status</span> = <span class="ruby-value str">""</span>
-506:
-507: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
-508: <span class="ruby-identifier">status</span> = <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>
-509: <span class="ruby-keyword kw">end</span>
-510:
-511: <span class="ruby-identifier">status</span> = <span class="ruby-node">"#{status};#{tmpdir_path}\n"</span>
-512:
-513: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
-514: <span class="ruby-identifier">fh</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">status</span>
-515: <span class="ruby-keyword kw">end</span>
-516: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-instance-method-details" class="method-section section">
- <h3 class="section-header">Private Instance Methods</h3>
-
-
- <div id="path-method" class="method-detail ">
- <a name="method-i-path"></a>
-
- <div class="method-heading">
-
- <span class="method-name">path</span><span
- class="method-args">()</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Path to status file
-</p>
-
-
-
- <div class="method-source-code"
- id="path-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 554</span>
-554: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">path</span>
-555: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
-556: <span class="ruby-identifier">script</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-identifier">$0</span>)
-557: <span class="ruby-identifier">pid</span> = <span class="ruby-identifier">$$</span>
-558: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_TMP"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/"</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">user</span>, <span class="ruby-identifier">script</span>, <span class="ruby-identifier">pid</span>, <span class="ruby-value str">"status"</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"."</span>)
-559: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="time-diff-method" class="method-detail ">
- <a name="method-i-time_diff"></a>
-
- <div class="method-heading">
-
- <span class="method-name">time_diff</span><span
- class="method-args">(t0, t1)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Get the elapsed time from the difference between two time stamps.
-</p>
-
-
-
- <div class="method-source-code"
- id="time-diff-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 562</span>
-562: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">time_diff</span>(<span class="ruby-identifier">t0</span>, <span class="ruby-identifier">t1</span>)
-563: <span class="ruby-constant">Time</span>.<span class="ruby-identifier">at</span>((<span class="ruby-constant">DateTime</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-identifier">t1</span>).<span class="ruby-identifier">to_time</span> <span class="ruby-operator">-</span> <span class="ruby-constant">DateTime</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-identifier">t0</span>).<span class="ruby-identifier">to_time</span>).<span class="ruby-identifier">to_i</span>).<span class="ruby-identifier">gmtime</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">'%X'</span>)
-564: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
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-
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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- <div id="classindex-section" class="section project-section">
- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
- <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
- <fieldset>
- <legend>Quicksearch</legend>
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- <li><a href="./Base36.html">Base36</a></li>
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- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="open-method" class="method-detail ">
- <a name="method-c-open"></a>
-
- <div class="method-heading">
-
- <span class="method-name">open</span><span
- class="method-args">(options, mode, stdio)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open <a href="Biopieces.html">Biopieces</a> output data stream for reading
-from stdin or a file specified in options[:stream_in] OR writing to stdout
-or a file specified in options[:stream_out] or options[:data_out].
-</p>
-
-
-
- <div class="method-source-code"
- id="open-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 572</span>
-572: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">options</span>, <span class="ruby-identifier">mode</span>, <span class="ruby-identifier">stdio</span>)
-573: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"r"</span>
-574: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:data_in</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:data_in</span>].<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
-575: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>([<span class="ruby-value str">"-"</span>])
-576: <span class="ruby-keyword kw">else</span>
-577: <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_in</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
-578: <span class="ruby-keyword kw">end</span>
-579: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"w"</span>
-580: <span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_out</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_out</span>], <span class="ruby-identifier">options</span>[<span class="ruby-value">:compress</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
-581: <span class="ruby-keyword kw">else</span>
-582: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad mode #{mode}"</span>
-583: <span class="ruby-keyword kw">end</span>
-584: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="private-class-method-details" class="method-section section">
- <h3 class="section-header">Private Class Methods</h3>
-
-
- <div id="nread-method" class="method-detail ">
- <a name="method-c-nread"></a>
-
- <div class="method-heading">
-
- <span class="method-name">nread</span><span
- class="method-args">(files)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a list of files for reading and return an <em>io</em> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="nread-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 616</span>
-616: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>(<span class="ruby-identifier">files</span>)
-617: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-value str">"cat "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">' '</span>));
-618: <span class="ruby-identifier">stdin</span>.<span class="ruby-identifier">close</span>
-619: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
-620: <span class="ruby-identifier">stdout</span>
-621: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="nwrite-method" class="method-detail ">
- <a name="method-c-nwrite"></a>
-
- <div class="method-heading">
-
- <span class="method-name">nwrite</span><span
- class="method-args">(file)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a file for writing and return an <em>io</em> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="nwrite-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 624</span>
-624: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nwrite</span>(<span class="ruby-identifier">file</span>)
-625: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>)
-626: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="read-method" class="method-detail ">
- <a name="method-c-read"></a>
-
- <div class="method-heading">
-
- <span class="method-name">read</span><span
- class="method-args">(files)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a reads stream to a list of files.
-</p>
-
-
-
- <div class="method-source-code"
- id="read-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 589</span>
-589: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">files</span>)
-590: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-comment cmt">#TODO case/when</span>
-591: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zipped?</span>(<span class="ruby-identifier">files</span>) <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zread</span>(<span class="ruby-identifier">files</span>) <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>(<span class="ruby-identifier">files</span>)
-592: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="write-method" class="method-detail ">
- <a name="method-c-write"></a>
-
- <div class="method-heading">
-
- <span class="method-name">write</span><span
- class="method-args">(file, zip=nil)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a write stream to a file and returns a <em>io</em> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="write-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 595</span>
-595: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">zip</span>=<span class="ruby-keyword kw">nil</span>)
-596: <span class="ruby-identifier">zip</span> <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zwrite</span>(<span class="ruby-identifier">file</span>) <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nwrite</span>(<span class="ruby-identifier">file</span>)
-597: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="zipped--method" class="method-detail ">
- <a name="method-c-zipped%3F"></a>
-
- <div class="method-heading">
-
- <span class="method-name">zipped?</span><span
- class="method-args">(files)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Test if a list of files are gzipped or not. Raises if files are mixed
-zipped and unzipped.
-</p>
-
-
-
- <div class="method-source-code"
- id="zipped--source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 630</span>
-630: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zipped?</span>(<span class="ruby-identifier">files</span>)
-631: <span class="ruby-identifier">type_hash</span> = {}
-632:
-633: <span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
-634: <span class="ruby-identifier">type</span> = <span class="ruby-node">`file #{file}`</span>
-635:
-636: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/gzip compressed/</span>
-637: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:gzip</span>] = <span class="ruby-keyword kw">true</span>
-638: <span class="ruby-keyword kw">else</span>
-639: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:ascii</span>] = <span class="ruby-keyword kw">true</span>
-640: <span class="ruby-keyword kw">end</span>
-641: <span class="ruby-keyword kw">end</span>
-642:
-643: <span class="ruby-identifier">raise</span> <span class="ruby-value str">"Mixture of zipped and unzipped files"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type_hash</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span>
-644:
-645: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:gzip</span>]
-646: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="zread-method" class="method-detail ">
- <a name="method-c-zread"></a>
-
- <div class="method-heading">
-
- <span class="method-name">zread</span><span
- class="method-args">(files)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a list of gzipped files for reading and return an <em>io</em> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="zread-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 600</span>
-600: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zread</span>(<span class="ruby-identifier">files</span>)
-601: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-value str">"zcat "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">' '</span>));
-602: <span class="ruby-identifier">stdin</span>.<span class="ruby-identifier">close</span>
-603: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
-604: <span class="ruby-identifier">stdout</span>
-605: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="zwrite-method" class="method-detail ">
- <a name="method-c-zwrite"></a>
-
- <div class="method-heading">
-
- <span class="method-name">zwrite</span><span
- class="method-args">(file)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Opens a file for gzipped writing and return an <em>io</em> object.
-</p>
-
-
-
- <div class="method-source-code"
- id="zwrite-source">
-<pre>
- <span class="ruby-comment cmt"># File biopieces.rb, line 608</span>
-608: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zwrite</span>(<span class="ruby-identifier">file</span>)
-609: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-node">"gzip -f > #{file}"</span>)
-610: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
-611: <span class="ruby-identifier">stdout</span>.<span class="ruby-identifier">close</span>
-612: <span class="ruby-identifier">stdin</span>
-613: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
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-
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- <div id="rdoc-debugging-section-dump" class="debugging-section">
-
- <p>Disabled; run with --debug to generate this.</p>
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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-<?xml version="1.0" encoding="utf-8"?>
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- <ul>
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- <li><a href="./bits_rb.html?TB_iframe=true&height=550&width=785"
- class="thickbox" title="bits.rb">bits.rb</a></li>
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- <h3 class="section-header">Parent</h3>
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- <h3 class="section-header">Methods</h3>
- <ul class="link-list">
-
- <li><a href="#method-c-hamming_dist">::hamming_dist</a></li>
-
- <li><a href="#method-i-%26">#&</a></li>
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- <h3 class="section-header">Class Index
- <span class="search-toggle"><img src="./images/find.png"
- height="16" width="16" alt="[+]"
- title="show/hide quicksearch" /></span></h3>
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- <legend>Quicksearch</legend>
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- class="quicksearch-field" />
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- <li><a href="./Base36.html">Base36</a></li>
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-
- <div id="documentation">
- <h1 class="class">String</h1>
-
- <div id="description">
- <p>
-Monkey patching Class <a href="String.html">String</a> to add bitwise
-operators. Behaviour matching Perl’s: <a
-href="http://perldoc.perl.org/perlop.html#Bitwise-String-Operators">perldoc.perl.org/perlop.html#Bitwise-String-Operators</a>
-</p>
-
- </div>
-
- <!-- Constants -->
-
-
- <!-- Attributes -->
-
-
- <!-- Methods -->
-
- <div id="public-class-method-details" class="method-section section">
- <h3 class="section-header">Public Class Methods</h3>
-
-
- <div id="hamming-dist-method" class="method-detail ">
- <a name="method-c-hamming_dist"></a>
-
- <div class="method-heading">
-
- <span class="method-name">hamming_dist</span><span
- class="method-args">(str1, str2)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to that returns the case senstive Hamming Distance between two
-strings. <a
-href="http://en.wikipedia.org/wiki/Hamming_distance">en.wikipedia.org/wiki/Hamming_distance</a>
-</p>
-
-
-
- <div class="method-source-code"
- id="hamming-dist-source">
-<pre>
- <span class="ruby-comment cmt"># File bits.rb, line 34</span>
-34: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hamming_dist</span>(<span class="ruby-identifier">str1</span>, <span class="ruby-identifier">str2</span>)
-35: <span class="ruby-identifier">raise</span> <span class="ruby-constant">StringError</span>, <span class="ruby-node">"Uneven string lengths: #{str1.length} != #{str2.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">str1</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">str2</span>.<span class="ruby-identifier">length</span>
-36: (<span class="ruby-identifier">str1</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">str2</span> ).<span class="ruby-identifier">count</span>(<span class="ruby-value str">"\x01-\xff"</span>)
-37: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- </div>
-
- <div id="public-instance-method-details" class="method-section section">
- <h3 class="section-header">Public Instance Methods</h3>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%26"></a>
-
- <div class="method-heading">
-
- <span class="method-name">&</span><span
- class="method-args">(str)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that performs bitwise AND operation where bits are copied if they
-exists in BOTH operands. If the operand sizes are different, the &
-operator methods acts as though the longer operand were truncated to the
-length of the shorter.
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bits.rb, line 43</span>
-43: <span class="ruby-keyword kw">def</span> &(<span class="ruby-identifier">str</span>)
-44: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
-45:
-46: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
-47: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
-48: <span class="ruby-keyword kw">end</span>
-49:
-50: <span class="ruby-identifier">new</span>
-51: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%5E"></a>
-
- <div class="method-heading">
-
- <span class="method-name">^</span><span
- class="method-args">(str)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that performs bitwise XOR operation where bits are copied if they
-exists in ONE BUT NOT BOTH operands.
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bits.rb, line 77</span>
-77: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">^</span>(<span class="ruby-identifier">str</span>)
-78: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
-79:
-80: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
-81: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
-82: <span class="ruby-keyword kw">end</span>
-83:
-84: <span class="ruby-identifier">new</span>
-85: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
- </div>
-
-
-
-
- </div>
-
-
- <div id="--method" class="method-detail ">
- <a name="method-i-%7C"></a>
-
- <div class="method-heading">
-
- <span class="method-name">|</span><span
- class="method-args">(str)</span>
- <span class="method-click-advice">click to toggle source</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that performs bitwise OR operation where bits are copied if they
-exists in EITHER operands. If the operand sizes differ, the shorter operand
-is extended with the terminal part of the longer operand.
-</p>
-
-
-
- <div class="method-source-code"
- id="--source">
-<pre>
- <span class="ruby-comment cmt"># File bits.rb, line 57</span>
-57: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">|</span>(<span class="ruby-identifier">str</span>)
-58: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
-59:
-60: <span class="ruby-identifier">min</span> = [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>
-61:
-62: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
-63: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
-64: <span class="ruby-keyword kw">end</span>
-65:
-66: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>
-67: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> <span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">min</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>]
-68: <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>
-69: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">min</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>]
-70: <span class="ruby-keyword kw">end</span>
-71:
-72: <span class="ruby-identifier">new</span>
-73: <span class="ruby-keyword kw">end</span></pre>
- </div>
-
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-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: boulder.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-03-19 09:17:13 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>filesys</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Biopieces [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Biopieces</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Object
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-<a href="Biopieces.html">Biopieces</a> are command line scripts and uses
-OptionParser to parse command line options according to a list of casts.
-Each cast prescribes the long and short name of the option, the type, if it
-is mandatory, the default value, and allowed and disallowed values. An
-optional list of extra casts can be supplied, and the integrity of the
-casts are checked. Following the command line parsing, the options are
-checked according to the casts. Methods are also included for handling the
-parsing and emitting of Biopiece records, which are ASCII text records
-consisting of lines with a key/value pair seperated by a colon and a white
-space ’: ’. Each record is separated by a line with three
-dashes ’—’.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000004">each</a>
-
- <a href="#M000003">each_record</a>
-
- <a href="#M000006">mktmpdir</a>
-
- <a href="#M000001">new</a>
-
- <a href="#M000002">parse</a>
-
- <a href="#M000005">puts</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Class methods</h3>
-
-
- <div id="method-M000001" class="method-detail">
- <a name="M000001"></a>
-
- <div class="method-heading">
-
- <a href="Biopieces.src/M000001.html" target="Code" class="method-signature"
- onclick="popupCode('Biopieces.src/M000001.html');return false;">
-
- <span class="method-name">new</span><span class="method-args">(test=nil, input=STDIN, output=STDOUT)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize a Biopiece and write the status to file. Options are for testing
-purposes only.
-</p>
-
- </div>
- </div>
-
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000004" class="method-detail">
- <a name="M000004"></a>
-
- <div class="method-heading">
-
- <span class="method-name">each</span><span class="method-args">()</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Alias for <a href="Biopieces.html#M000003">each_record</a>
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000003" class="method-detail">
- <a name="M000003"></a>
-
- <div class="method-heading">
-
- <a href="Biopieces.src/M000003.html" target="Code" class="method-signature"
- onclick="popupCode('Biopieces.src/M000003.html');return false;">
-
- <span class="method-name">each_record</span><span class="method-args">() {|record unless record.empty?| ...}</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open Biopiece input stream if not open and iterate over all Biopiece
-records in the stream.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000006" class="method-detail">
- <a name="M000006"></a>
-
- <div class="method-heading">
-
- <a href="Biopieces.src/M000006.html" target="Code" class="method-signature"
- onclick="popupCode('Biopieces.src/M000006.html');return false;">
-
- <span class="method-name">mktmpdir</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Create a temporary directory inside the ENV[“BP_TMP“] dir.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000002" class="method-detail">
- <a name="M000002"></a>
-
- <div class="method-heading">
-
- <a href="Biopieces.src/M000002.html" target="Code" class="method-signature"
- onclick="popupCode('Biopieces.src/M000002.html');return false;">
-
- <span class="method-name">parse</span><span class="method-args">(argv, cast_list=[], script_path=$0)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check the integrity of a list of casts, followed by parsion options from
-argv and finally checking the options according to the casts. Returns nil
-if argv is empty, otherwise an options hash.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000005" class="method-detail">
- <a name="M000005"></a>
-
- <div class="method-heading">
-
- <a href="Biopieces.src/M000005.html" target="Code" class="method-signature"
- onclick="popupCode('Biopieces.src/M000005.html');return false;">
-
- <span class="method-name">puts</span><span class="method-args">(record)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open Biopiece output stream if not open and puts record to the stream.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>new (Biopieces)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 43</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">input</span>=<span class="ruby-constant">STDIN</span>, <span class="ruby-identifier">output</span>=<span class="ruby-constant">STDOUT</span>)
- <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
- <span class="ruby-ivar">@input</span> = <span class="ruby-identifier">input</span>
- <span class="ruby-ivar">@output</span> = <span class="ruby-identifier">output</span>
- <span class="ruby-ivar">@status</span> = <span class="ruby-constant">Status</span>.<span class="ruby-identifier">new</span>
- <span class="ruby-ivar">@status</span>.<span class="ruby-identifier">set</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@test</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>parse (Biopieces)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 54</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">parse</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">cast_list</span>=[], <span class="ruby-identifier">script_path</span>=<span class="ruby-identifier">$0</span>)
- <span class="ruby-identifier">casts</span> = <span class="ruby-constant">Casts</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">cast_list</span>)
- <span class="ruby-identifier">option_handler</span> = <span class="ruby-constant">OptionHandler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-ivar">@test</span>)
- <span class="ruby-ivar">@options</span> = <span class="ruby-identifier">option_handler</span>.<span class="ruby-identifier">options_parse</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>each_record (Biopieces)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 62</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_record</span>
- <span class="ruby-ivar">@in</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>, <span class="ruby-ivar">@input</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">nil?</span>
-
- <span class="ruby-identifier">record</span> = {}
-
- <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
- <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">line</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^([^:]+): (.*)$/</span>
- <span class="ruby-identifier">record</span>[<span class="ruby-identifier">$1</span>] = <span class="ruby-identifier">$2</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^---$/</span>
- <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
- <span class="ruby-identifier">record</span> = {}
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad record format: #{line}"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
-
- <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>puts (Biopieces)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 88</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
- <span class="ruby-ivar">@out</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>, <span class="ruby-ivar">@output</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
-
- <span class="ruby-identifier">record</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>,<span class="ruby-identifier">value</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{key}: #{value}\n"</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-value str">"---\n"</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>mktmpdir (Biopieces)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 99</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mktmpdir</span>
- <span class="ruby-identifier">time</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">now</span>.<span class="ruby-identifier">to_i</span>
- <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
- <span class="ruby-identifier">pid</span> = <span class="ruby-identifier">$$</span>
- <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_TMP"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/"</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">user</span>, <span class="ruby-identifier">time</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pid</span>, <span class="ruby-identifier">pid</span>, <span class="ruby-value str">"bp_tmp"</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"_"</span>)
- <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">mkdir</span>(<span class="ruby-identifier">path</span>)
- <span class="ruby-ivar">@status</span>.<span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">path</span>)
- <span class="ruby-identifier">path</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: CastError [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">CastError</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- StandardError
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Error class for all exceptions to do with option casts.
-</p>
-
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Casts [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Casts</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Array
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class to handle casts of command line options. Each cast prescribes the
-long and short name of the option, the type, if it is mandatory, the
-default value, and allowed and disallowed values. An optional list of extra
-casts can be supplied, and the integrity of the casts are checked.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000007">new</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
- <div id="constants-list">
- <h3 class="section-bar">Constants</h3>
-
- <div class="name-list">
- <table summary="Constants">
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">TYPES</td>
- <td>=</td>
- <td class="context-item-value">%w[flag string list int uint float file file! files files! dir dir! genome]</td>
-
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">MANDATORY</td>
- <td>=</td>
- <td class="context-item-value">%w[long short type mandatory default allowed disallowed]</td>
-
- </tr>
-
- </table>
- </div>
- </div>
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Class methods</h3>
-
-
- <div id="method-M000007" class="method-detail">
- <a name="M000007"></a>
-
- <div class="method-heading">
-
- <a href="Casts.src/M000007.html" target="Code" class="method-signature"
- onclick="popupCode('Casts.src/M000007.html');return false;">
-
- <span class="method-name">new</span><span class="method-args">(cast_list=[])</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Initialize cast object with an optional options cast list to which
-ubiquitous casts are added after which all casts are checked.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>new (Casts)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 125</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">cast_list</span>=[])
- <span class="ruby-ivar">@cast_list</span> = <span class="ruby-identifier">cast_list</span>
- <span class="ruby-identifier">ubiquitous</span>
- <span class="ruby-identifier">check</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">push</span> <span class="ruby-operator">*</span><span class="ruby-ivar">@cast_list</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Fasta [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Fasta</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/fasta_rb.html">
-
- fasta.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Object
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000003">close</a>
-
- <a href="#M000004">each</a>
-
- <a href="#M000005">get_entry</a>
-
- <a href="#M000002">new</a>
-
- <a href="#M000001">open</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="includes">
- <h3 class="section-bar">Included Modules</h3>
-
- <div id="includes-list">
-
- <span class="include-name">Enumerable</span>
-
- </div>
- </div>
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Class methods</h3>
-
-
- <div id="method-M000002" class="method-detail">
- <a name="M000002"></a>
-
- <div class="method-heading">
-
- <a href="Fasta.src/M000002.html" target="Code" class="method-signature"
- onclick="popupCode('Fasta.src/M000002.html');return false;">
-
- <span class="method-name">new</span><span class="method-args">(io, type=nil)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- </div>
- </div>
-
-
- <div id="method-M000001" class="method-detail">
- <a name="M000001"></a>
-
- <div class="method-heading">
-
- <a href="Fasta.src/M000001.html" target="Code" class="method-signature"
- onclick="popupCode('Fasta.src/M000001.html');return false;">
-
- <span class="method-name">open</span><span class="method-args">(*args) {|ios| ...}</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Class method allowing open to be used on (zipped) files. See File.open.
-</p>
-
- </div>
- </div>
-
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000003" class="method-detail">
- <a name="M000003"></a>
-
- <div class="method-heading">
-
- <a href="Fasta.src/M000003.html" target="Code" class="method-signature"
- onclick="popupCode('Fasta.src/M000003.html');return false;">
-
- <span class="method-name">close</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to close ios.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000004" class="method-detail">
- <a name="M000004"></a>
-
- <div class="method-heading">
-
- <a href="Fasta.src/M000004.html" target="Code" class="method-signature"
- onclick="popupCode('Fasta.src/M000004.html');return false;">
-
- <span class="method-name">each</span><span class="method-args">() {|entry| ...}</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Iterator method for parsing FASTA enries.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000005" class="method-detail">
- <a name="M000005"></a>
-
- <div class="method-heading">
-
- <a href="Fasta.src/M000005.html" target="Code" class="method-signature"
- onclick="popupCode('Fasta.src/M000005.html');return false;">
-
- <span class="method-name">get_entry</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to get the next FASTA entry form an ios and return this as a Seq
-object. If no entry is found or eof then nil is returned.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>open (Fasta)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File fasta.rb, line 33</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">args</span>)
- <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">args</span>)
- <span class="ruby-identifier">fasta</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
-
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
- <span class="ruby-keyword kw">begin</span>
- <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">fasta</span>
- <span class="ruby-keyword kw">ensure</span>
- <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">fasta</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>new (Fasta)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File fasta.rb, line 50</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>, <span class="ruby-identifier">type</span>=<span class="ruby-keyword kw">nil</span>)
- <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
- <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>each (Fasta)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File fasta.rb, line 56</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
- <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
- <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">entry</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>get_entry (Fasta)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File fasta.rb, line 64</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
- <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
-
- <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
-
- (<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>) = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span>(<span class="ruby-identifier">$/</span>, <span class="ruby-value">2</span>)
-
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
-
- <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
- <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">type</span> = <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-value">? </span><span class="ruby-keyword kw">nil</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">downcase</span>
- <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp re">/\s/</span>, <span class="ruby-value str">''</span>)
- <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span> = <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/^>/</span>, <span class="ruby-value str">''</span>).<span class="ruby-identifier">rstrip</span>
-
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">empty?</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">empty?</span>
-
- <span class="ruby-identifier">entry</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: FastaError [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">FastaError</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/fasta_rb.html">
-
- fasta.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- StandardError
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Error class for all exceptions to do with FASTA.
-</p>
-
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: OptionHandler [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">OptionHandler</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Object
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class for parsing argv using OptionParser according to given casts. Default
-options are set, file glob expressions expanded, and options are checked
-according to the casts. Usage information is printed and exit called if
-required.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000008">new</a>
-
- <a href="#M000016">options_check</a>
-
- <a href="#M000023">options_check_allowed</a>
-
- <a href="#M000022">options_check_dir</a>
-
- <a href="#M000024">options_check_disallowed</a>
-
- <a href="#M000020">options_check_file</a>
-
- <a href="#M000021">options_check_files</a>
-
- <a href="#M000018">options_check_int</a>
-
- <a href="#M000017">options_check_mandatory</a>
-
- <a href="#M000019">options_check_uint</a>
-
- <a href="#M000014">options_default</a>
-
- <a href="#M000015">options_glob</a>
-
- <a href="#M000009">options_parse</a>
-
- <a href="#M000013">print_usage_and_exit</a>
-
- <a href="#M000011">print_usage_full?</a>
-
- <a href="#M000012">print_usage_short?</a>
-
- <a href="#M000010">wiki_path</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
- <div id="constants-list">
- <h3 class="section-bar">Constants</h3>
-
- <div class="name-list">
- <table summary="Constants">
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">REGEX_LIST</td>
- <td>=</td>
- <td class="context-item-value">/^(list|files|files!)$/</td>
-
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">REGEX_INT</td>
- <td>=</td>
- <td class="context-item-value">/^(int|uint)$/</td>
-
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">REGEX_STRING</td>
- <td>=</td>
- <td class="context-item-value">/^(string|file|file!|dir|dir!|genome)$/</td>
-
- </tr>
-
- </table>
- </div>
- </div>
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Class methods</h3>
-
-
- <div id="method-M000008" class="method-detail">
- <a name="M000008"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000008.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000008.html');return false;">
-
- <span class="method-name">new</span><span class="method-args">(argv, casts, script_path, test=nil)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- </div>
- </div>
-
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000016" class="method-detail">
- <a name="M000016"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000016.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000016.html');return false;">
-
- <span class="method-name">options_check</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check all options according to casts.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000023" class="method-detail">
- <a name="M000023"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000023.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000023.html');return false;">
-
- <span class="method-name">options_check_allowed</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check options and raise unless allowed.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000022" class="method-detail">
- <a name="M000022"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000022.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000022.html');return false;">
-
- <span class="method-name">options_check_dir</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check dir! type argument and raise if directory don’t exist.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000024" class="method-detail">
- <a name="M000024"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000024.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000024.html');return false;">
-
- <span class="method-name">options_check_disallowed</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check disallowed argument values and raise if disallowed.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000020" class="method-detail">
- <a name="M000020"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000020.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000020.html');return false;">
-
- <span class="method-name">options_check_file</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check file! type argument and raise if file don’t exists.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000021" class="method-detail">
- <a name="M000021"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000021.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000021.html');return false;">
-
- <span class="method-name">options_check_files</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check files! type argument and raise if files don’t exists.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000018" class="method-detail">
- <a name="M000018"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000018.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000018.html');return false;">
-
- <span class="method-name">options_check_int</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check int type option and raise if not an integer.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000017" class="method-detail">
- <a name="M000017"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000017.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000017.html');return false;">
-
- <span class="method-name">options_check_mandatory</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if a mandatory option is set and raise if it isn’t.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000019" class="method-detail">
- <a name="M000019"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000019.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000019.html');return false;">
-
- <span class="method-name">options_check_uint</span><span class="method-args">(cast)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check uint type option and raise if not an unsinged integer.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000014" class="method-detail">
- <a name="M000014"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000014.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000014.html');return false;">
-
- <span class="method-name">options_default</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Set default options value from cast unless a value is set.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000015" class="method-detail">
- <a name="M000015"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000015.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000015.html');return false;">
-
- <span class="method-name">options_glob</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Expands glob expressions to a full list of paths. Examples:
-“*.fna” or “foo.fna,*.fna” or
-“foo.fna,/bar/*.fna“
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000009" class="method-detail">
- <a name="M000009"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000009.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000009.html');return false;">
-
- <span class="method-name">options_parse</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Parse options from argv using OptionParser and casts denoting long and
-short option names. Usage information is printed and exit called. A hash
-with options is returned.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000013" class="method-detail">
- <a name="M000013"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000013.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000013.html');return false;">
-
- <span class="method-name">print_usage_and_exit</span><span class="method-args">(full=nil)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Print usage info by Calling an external script ‘print_wiki’
-using a system() call and exit. An optional ‘full’ flag outputs
-the full usage info.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000011" class="method-detail">
- <a name="M000011"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000011.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000011.html');return false;">
-
- <span class="method-name">print_usage_full?</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if full “usage info” should be printed.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000012" class="method-detail">
- <a name="M000012"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000012.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000012.html');return false;">
-
- <span class="method-name">print_usage_short?</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Check if short “usage info” should be printed.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000010" class="method-detail">
- <a name="M000010"></a>
-
- <div class="method-heading">
-
- <a href="OptionHandler.src/M000010.html" target="Code" class="method-signature"
- onclick="popupCode('OptionHandler.src/M000010.html');return false;">
-
- <span class="method-name">wiki_path</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Given the script name determine the path of the wiki file with the usage
-info.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>new (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 250</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>)
- <span class="ruby-ivar">@argv</span> = <span class="ruby-identifier">argv</span>
- <span class="ruby-ivar">@casts</span> = <span class="ruby-identifier">casts</span>
- <span class="ruby-ivar">@script_path</span> = <span class="ruby-identifier">script_path</span>
- <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_parse (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 260</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_parse</span>
- <span class="ruby-ivar">@options</span> = {}
-
- <span class="ruby-identifier">option_parser</span> = <span class="ruby-constant">OptionParser</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">option</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
- <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>]
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'flag'</span>
- <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]}"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">o</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">o</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'float'</span>
- <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} F"</span>, <span class="ruby-constant">Float</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">f</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_LIST</span>
- <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>( <span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} A"</span>, <span class="ruby-constant">Array</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">a</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_INT</span>
- <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} I"</span>, <span class="ruby-constant">Integer</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">i</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_STRING</span>
- <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} S"</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">s</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Unknown option type: '#{cast[:type]}'"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-identifier">option_parser</span>.<span class="ruby-identifier">parse!</span>(<span class="ruby-ivar">@argv</span>)
-
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">print_usage_full?</span>
- <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-keyword kw">true</span>)
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">print_usage_short?</span>
- <span class="ruby-identifier">print_usage_and_exit</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-identifier">options_default</span>
- <span class="ruby-identifier">options_glob</span>
- <span class="ruby-identifier">options_check</span>
-
- <span class="ruby-ivar">@options</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>wiki_path (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 308</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">wiki_path</span>
- <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_DIR"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/bp_usage/"</span> <span class="ruby-operator">+</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-ivar">@script_path</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">".wiki"</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-node">"No such wiki file: #{path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">path</span>
- <span class="ruby-identifier">path</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>print_usage_full? (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 315</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_full?</span>
- <span class="ruby-ivar">@options</span>[<span class="ruby-value str">"help"</span>]
- <span class="ruby-keyword kw">end</span></pre>
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-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>print_usage_short? (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 320</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_short?</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value str">"stream_in"</span>]
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value str">"data_in"</span>]
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">wiki_path</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/</span> <span class="ruby-comment cmt"># TODO get rid of this!</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-</html>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>print_usage_and_exit (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 337</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-identifier">full</span>=<span class="ruby-keyword kw">nil</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@test</span>
- <span class="ruby-keyword kw">return</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">full</span>
- <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path} --help"</span>)
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path}"</span>)
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-identifier">raise</span> <span class="ruby-node">"Failed printing wiki: #{wiki_path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">success?</span>
-
- <span class="ruby-identifier">exit</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_default (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 354</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_default</span>
- <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:default</span>]
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:default</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_glob (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 364</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_glob</span>
- <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files'</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-identifier">files</span> = []
-
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">path</span>.<span class="ruby-identifier">include?</span> <span class="ruby-value str">"*"</span>
- <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">glob</span>(<span class="ruby-identifier">path</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">file</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">file</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">path</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] = <span class="ruby-identifier">files</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 387</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check</span>
- <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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-<head>
- <title>options_check_mandatory (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 401</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:mandatory</span>]
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Mandatory argument: --#{cast[:long]}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_int (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 408</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'int'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_uint (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 417</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'uint'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]] <span class="ruby-operator">>=</span> <span class="ruby-value">0</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_file (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 426</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'file!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such file: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]]
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_files (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 433</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such file: '#{path}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">path</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_dir (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 442</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'dir!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such directory: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]]
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_allowed (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 449</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:allowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-identifier">allowed_hash</span> = {}
- <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:allowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">allowed_hash</span>[<span class="ruby-identifier">a</span>.<span class="ruby-identifier">to_s</span>] = <span class="ruby-value">1</span> }
-
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">allowed_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">to_s</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>options_check_disallowed (OptionHandler)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 459</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:disallowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]
- <span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:disallowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">val</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-identifier">:long</span>]].<span class="ruby-identifier">to_s</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Seq [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Seq</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Object
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000043">complement</a>
-
- <a href="#M000044">generate</a>
-
- <a href="#M000037">is_dna</a>
-
- <a href="#M000039">is_protein</a>
-
- <a href="#M000038">is_rna</a>
-
- <a href="#M000036">len</a>
-
- <a href="#M000035">length</a>
-
- <a href="#M000042">to_bp</a>
-
- <a href="#M000041">to_dna</a>
-
- <a href="#M000040">to_rna</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
- <div id="attribute-list">
- <h3 class="section-bar">Attributes</h3>
-
- <div class="name-list">
- <table>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">qual</td>
-
- <td class="context-item-value"> [RW] </td>
-
- <td class="context-item-desc"></td>
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">seq</td>
-
- <td class="context-item-value"> [RW] </td>
-
- <td class="context-item-desc"></td>
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">seq_name</td>
-
- <td class="context-item-value"> [RW] </td>
-
- <td class="context-item-desc"></td>
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">type</td>
-
- <td class="context-item-value"> [RW] </td>
-
- <td class="context-item-desc"></td>
- </tr>
-
- </table>
- </div>
- </div>
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000043" class="method-detail">
- <a name="M000043"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000043.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000043.html');return false;">
-
- <span class="method-name">complement</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that complements sequence including ambiguity codes.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000044" class="method-detail">
- <a name="M000044"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000044.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000044.html');return false;">
-
- <span class="method-name">generate</span><span class="method-args">(length,type)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that generates a random sequence of a given length.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000037" class="method-detail">
- <a name="M000037"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000037.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000037.html');return false;">
-
- <span class="method-name">is_dna</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns true is a given sequence type is DNA.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000039" class="method-detail">
- <a name="M000039"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000039.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000039.html');return false;">
-
- <span class="method-name">is_protein</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- </div>
- </div>
-
-
- <div id="method-M000038" class="method-detail">
- <a name="M000038"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000038.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000038.html');return false;">
-
- <span class="method-name">is_rna</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- </div>
- </div>
-
-
- <div id="method-M000036" class="method-detail">
- <a name="M000036"></a>
-
- <div class="method-heading">
-
- <span class="method-name">len</span><span class="method-args">()</span>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Alias for <a href="Seq.html#M000035">length</a>
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000035" class="method-detail">
- <a name="M000035"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000035.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000035.html');return false;">
-
- <span class="method-name">length</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- </div>
- </div>
-
-
- <div id="method-M000042" class="method-detail">
- <a name="M000042"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000042.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000042.html');return false;">
-
- <span class="method-name">to_bp</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that given a <a href="Seq.html">Seq</a> entry returns a <a
-href="Biopieces.html">Biopieces</a> record (a hash).
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000041" class="method-detail">
- <a name="M000041"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000041.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000041.html');return false;">
-
- <span class="method-name">to_dna</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to reverse-transcribe RNA to DNA.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000040" class="method-detail">
- <a name="M000040"></a>
-
- <div class="method-heading">
-
- <a href="Seq.src/M000040.html" target="Code" class="method-signature"
- onclick="popupCode('Seq.src/M000040.html');return false;">
-
- <span class="method-name">to_rna</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to transcribe DNA to RNA.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>length (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 11</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">length</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-value">? </span><span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">length</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_dna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 18</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'dna'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_rna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 22</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'rna'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_protein (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 26</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'protein'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_rna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 31</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Tt'</span>,<span class="ruby-value str">'Uu'</span>)
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_dna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 39</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot reverse-transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot reverse-transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Uu'</span>,<span class="ruby-value str">'Tt'</span>)
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>complement (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 47</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot complement 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-
- <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>generate (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 60</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>(<span class="ruby-identifier">length</span>,<span class="ruby-identifier">type</span>)
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative sequence length: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-
- <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-identifier">seq_new</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">length</span>) { <span class="ruby-identifier">alph</span>[<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span>)] }.<span class="ruby-identifier">join</span>(<span class="ruby-value str">""</span>)
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
-
- <span class="ruby-identifier">seq_new</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>guess_type (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 4</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">guess_type</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">"No sequence."</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">empty?</span>
-
- <span class="ruby-identifier">seq_beg</span> = <span class="ruby-keyword kw">self</span>[ <span class="ruby-value">0</span>, <span class="ruby-value">100</span> ].<span class="ruby-identifier">upcase</span>
-
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq_beg</span>.<span class="ruby-identifier">count</span>( <span class="ruby-value str">"FLPQIE"</span> ) <span class="ruby-operator">></span> <span class="ruby-value">0</span>
- <span class="ruby-constant">Seq</span><span class="ruby-operator">::</span><span class="ruby-constant">AA</span>.<span class="ruby-identifier">new</span>( <span class="ruby-keyword kw">self</span> )
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">seq_beg</span>.<span class="ruby-identifier">count</span>( <span class="ruby-value str">"U"</span> ) <span class="ruby-operator">></span> <span class="ruby-value">0</span>
- <span class="ruby-constant">Seq</span><span class="ruby-operator">::</span><span class="ruby-constant">NA</span><span class="ruby-operator">::</span><span class="ruby-constant">RNA</span>.<span class="ruby-identifier">new</span>( <span class="ruby-keyword kw">self</span> )
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-constant">Seq</span><span class="ruby-operator">::</span><span class="ruby-constant">NA</span><span class="ruby-operator">::</span><span class="ruby-constant">DNA</span>.<span class="ruby-identifier">new</span>( <span class="ruby-keyword kw">self</span> )
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>wrap (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 19</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">wrap</span>( <span class="ruby-identifier">width</span> = <span class="ruby-value">80</span>, <span class="ruby-identifier">delimit</span> = <span class="ruby-value str">"\n"</span> )
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Cannot wrap sequence to negative width: #{ width }."</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">width</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">delete!</span>( <span class="ruby-value str">" \t\n\r"</span> )
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">gsub</span>( <span class="ruby-node">/.{#{ width }}(?!$)/</span>, <span class="ruby-node">"\\0#{ delimit }"</span> )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>wrap! (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 27</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">wrap!</span>( <span class="ruby-identifier">width</span> = <span class="ruby-value">80</span>, <span class="ruby-identifier">delimit</span> = <span class="ruby-value str">"\n"</span> )
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">replace</span>( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">wrap</span>( <span class="ruby-identifier">width</span>, <span class="ruby-identifier">delimit</span> ) )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>generate (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 32</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>( <span class="ruby-identifier">length</span> )
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Cannot generate negative sequence length: #{ length }."</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-
- <span class="ruby-identifier">alph</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">residues</span>
- <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>( <span class="ruby-identifier">length</span> ) { <span class="ruby-identifier">alph</span>[ <span class="ruby-identifier">rand</span>( <span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span> ) ] }.<span class="ruby-identifier">join</span>( <span class="ruby-value str">""</span> )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>length (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 11</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">length</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-value">? </span><span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">length</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_dna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 18</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'dna'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_rna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 22</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'rna'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>is_protein (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 26</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'protein'</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_rna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 31</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Tt'</span>,<span class="ruby-value str">'Uu'</span>)
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_dna (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 39</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot reverse-transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot reverse-transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Uu'</span>,<span class="ruby-value str">'Tt'</span>)
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_bp (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 47</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq_name"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
- <span class="ruby-identifier">record</span> = {}
- <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ_NAME'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
- <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
- <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ_LEN'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
- <span class="ruby-identifier">record</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>complement (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 58</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot complement 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
-
- <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>generate (Seq)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 71</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>(<span class="ruby-identifier">length</span>,<span class="ruby-identifier">type</span>)
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative sequence length: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
-
- <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
- <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
- <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-identifier">seq_new</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">length</span>) { <span class="ruby-identifier">alph</span>[<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span>)] }.<span class="ruby-identifier">join</span>(<span class="ruby-value str">""</span>)
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
- <span class="ruby-identifier">seq_new</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Seq::AA [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Seq::AA</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- <a href="../Seq.html">
-
- Seq
-
- </a>
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class containing methods specific for amino acid (<a href="AA.html">AA</a>)
-sequences.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000037">mol_weight</a>
-
- <a href="#M000036">residues</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000037" class="method-detail">
- <a name="M000037"></a>
-
- <div class="method-heading">
-
- <a href="AA.src/M000037.html" target="Code" class="method-signature"
- onclick="popupCode('AA.src/M000037.html');return false;">
-
- <span class="method-name">mol_weight</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Calculate the molecular weight of an amino acid seuqunce. The caluculation
-is only approximate since there is no correction for amino bond formation
-and the MW used are somewhat imprecise: <a
-href="http://www.expasy.ch/tools/pscale/Molecularweight.html">www.expasy.ch/tools/pscale/Molecularweight.html</a>
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000036" class="method-detail">
- <a name="M000036"></a>
-
- <div class="method-heading">
-
- <a href="AA.src/M000036.html" target="Code" class="method-signature"
- onclick="popupCode('AA.src/M000036.html');return false;">
-
- <span class="method-name">residues</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns an array of amino acid residues.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>residues (Seq::AA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 47</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">residues</span>
- <span class="ruby-node">%w{ F L S Y C W P H Q R I M T N K V A D E G }</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>mol_weight (Seq::AA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 55</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mol_weight</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"invalid residues found: #{self.delete("#{residues.join( "" )}")}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">upcase</span> <span class="ruby-operator">=~</span> <span class="ruby-node">/[^#{residues.join( "" )}]/</span>
-
- <span class="ruby-identifier">mol_weight_aa</span> = {
- <span class="ruby-value str">"A"</span> =<span class="ruby-operator">></span> <span class="ruby-value">89.000</span>, <span class="ruby-comment cmt"># Ala</span>
- <span class="ruby-value str">"R"</span> =<span class="ruby-operator">></span> <span class="ruby-value">174.000</span>, <span class="ruby-comment cmt"># Arg</span>
- <span class="ruby-value str">"N"</span> =<span class="ruby-operator">></span> <span class="ruby-value">132.000</span>, <span class="ruby-comment cmt"># Asn</span>
- <span class="ruby-value str">"D"</span> =<span class="ruby-operator">></span> <span class="ruby-value">133.000</span>, <span class="ruby-comment cmt"># Asp</span>
- <span class="ruby-value str">"C"</span> =<span class="ruby-operator">></span> <span class="ruby-value">121.000</span>, <span class="ruby-comment cmt"># Cys</span>
- <span class="ruby-value str">"Q"</span> =<span class="ruby-operator">></span> <span class="ruby-value">146.000</span>, <span class="ruby-comment cmt"># Gln</span>
- <span class="ruby-value str">"E"</span> =<span class="ruby-operator">></span> <span class="ruby-value">147.000</span>, <span class="ruby-comment cmt"># Glu</span>
- <span class="ruby-value str">"G"</span> =<span class="ruby-operator">></span> <span class="ruby-value">75.000</span>, <span class="ruby-comment cmt"># Gly</span>
- <span class="ruby-value str">"H"</span> =<span class="ruby-operator">></span> <span class="ruby-value">155.000</span>, <span class="ruby-comment cmt"># His</span>
- <span class="ruby-value str">"I"</span> =<span class="ruby-operator">></span> <span class="ruby-value">131.000</span>, <span class="ruby-comment cmt"># Ile</span>
- <span class="ruby-value str">"L"</span> =<span class="ruby-operator">></span> <span class="ruby-value">131.000</span>, <span class="ruby-comment cmt"># Leu</span>
- <span class="ruby-value str">"K"</span> =<span class="ruby-operator">></span> <span class="ruby-value">146.000</span>, <span class="ruby-comment cmt"># Lys</span>
- <span class="ruby-value str">"M"</span> =<span class="ruby-operator">></span> <span class="ruby-value">149.000</span>, <span class="ruby-comment cmt"># Met</span>
- <span class="ruby-value str">"F"</span> =<span class="ruby-operator">></span> <span class="ruby-value">165.000</span>, <span class="ruby-comment cmt"># Phe</span>
- <span class="ruby-value str">"P"</span> =<span class="ruby-operator">></span> <span class="ruby-value">115.000</span>, <span class="ruby-comment cmt"># Pro</span>
- <span class="ruby-value str">"S"</span> =<span class="ruby-operator">></span> <span class="ruby-value">105.000</span>, <span class="ruby-comment cmt"># Ser</span>
- <span class="ruby-value str">"T"</span> =<span class="ruby-operator">></span> <span class="ruby-value">119.000</span>, <span class="ruby-comment cmt"># Thr</span>
- <span class="ruby-value str">"W"</span> =<span class="ruby-operator">></span> <span class="ruby-value">204.000</span>, <span class="ruby-comment cmt"># Trp</span>
- <span class="ruby-value str">"Y"</span> =<span class="ruby-operator">></span> <span class="ruby-value">181.000</span>, <span class="ruby-comment cmt"># Tyr</span>
- <span class="ruby-value str">"V"</span> =<span class="ruby-operator">></span> <span class="ruby-value">117.000</span>, <span class="ruby-comment cmt"># Val</span>
- }
-
- <span class="ruby-identifier">mw</span> = <span class="ruby-value">0</span><span class="ruby-value">.0</span>
-
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> <span class="ruby-identifier">mw</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">mol_weight_aa</span>[ <span class="ruby-identifier">c</span> ] }
-
- <span class="ruby-identifier">mw</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Seq::NA [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Seq::NA</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- <a href="../Seq.html">
-
- Seq
-
- </a>
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class containing methods specific for nucleic acid (<a
-href="NA.html">NA</a>) sequences.
-</p>
-
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
- <div id="class-list">
- <h3 class="section-bar">Classes and Modules</h3>
-
- Class <a href="NA/DNA.html" class="link">Seq::NA::DNA</a><br />
-Class <a href="NA/RNA.html" class="link">Seq::NA::RNA</a><br />
-
- </div>
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Seq::NA::DNA [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Seq::NA::DNA</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../../../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- <a href="../NA.html">
-
- Seq::NA
-
- </a>
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class containing methods specific for <a href="DNA.html">DNA</a> sequences.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000040">complement</a>
-
- <a href="#M000038">residues</a>
-
- <a href="#M000039">to_RNA</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000040" class="method-detail">
- <a name="M000040"></a>
-
- <div class="method-heading">
-
- <a href="DNA.src/M000040.html" target="Code" class="method-signature"
- onclick="popupCode('DNA.src/M000040.html');return false;">
-
- <span class="method-name">complement</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that complements <a href="DNA.html">DNA</a> sequence including
-ambiguity codes.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000038" class="method-detail">
- <a name="M000038"></a>
-
- <div class="method-heading">
-
- <a href="DNA.src/M000038.html" target="Code" class="method-signature"
- onclick="popupCode('DNA.src/M000038.html');return false;">
-
- <span class="method-name">residues</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns an array of <a href="DNA.html">DNA</a> residues.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000039" class="method-detail">
- <a name="M000039"></a>
-
- <div class="method-heading">
-
- <a href="DNA.src/M000039.html" target="Code" class="method-signature"
- onclick="popupCode('DNA.src/M000039.html');return false;">
-
- <span class="method-name">to_RNA</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to transcribe <a href="DNA.html">DNA</a> to <a
-href="RNA.html">RNA</a>.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>residues (Seq::NA::DNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 94</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">residues</span>
- <span class="ruby-node">%w{ A T C G }</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_RNA (Seq::NA::DNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 99</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_RNA</span>
- <span class="ruby-constant">Seq</span><span class="ruby-operator">::</span><span class="ruby-constant">NA</span><span class="ruby-operator">::</span><span class="ruby-constant">RNA</span>.<span class="ruby-identifier">new</span>( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">tr</span>( <span class="ruby-value str">'Tt'</span>, <span class="ruby-value str">'Uu'</span> ) )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>complement (Seq::NA::DNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 104</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Seq::NA::RNA [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Seq::NA::RNA</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../../../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- <a href="../NA.html">
-
- Seq::NA
-
- </a>
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class containing methods specific for <a href="RNA.html">RNA</a> sequences.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000043">complement</a>
-
- <a href="#M000041">residues</a>
-
- <a href="#M000042">to_DNA</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000043" class="method-detail">
- <a name="M000043"></a>
-
- <div class="method-heading">
-
- <a href="RNA.src/M000043.html" target="Code" class="method-signature"
- onclick="popupCode('RNA.src/M000043.html');return false;">
-
- <span class="method-name">complement</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that complements <a href="RNA.html">RNA</a> sequence including
-ambiguity codes.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000041" class="method-detail">
- <a name="M000041"></a>
-
- <div class="method-heading">
-
- <a href="RNA.src/M000041.html" target="Code" class="method-signature"
- onclick="popupCode('RNA.src/M000041.html');return false;">
-
- <span class="method-name">residues</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method that returns an array of <a href="RNA.html">RNA</a> residues.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000042" class="method-detail">
- <a name="M000042"></a>
-
- <div class="method-heading">
-
- <a href="RNA.src/M000042.html" target="Code" class="method-signature"
- onclick="popupCode('RNA.src/M000042.html');return false;">
-
- <span class="method-name">to_DNA</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Method to reverse transcribe <a href="RNA.html">RNA</a> to <a
-href="DNA.html">DNA</a>.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>residues (Seq::NA::RNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 112</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">residues</span>
- <span class="ruby-node">%w{ A U C G }</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>to_DNA (Seq::NA::RNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 117</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_DNA</span>
- <span class="ruby-constant">Seq</span><span class="ruby-operator">::</span><span class="ruby-constant">NA</span><span class="ruby-operator">::</span><span class="ruby-constant">DNA</span>.<span class="ruby-identifier">new</span>( <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">tr</span>( <span class="ruby-value str">'Uu'</span>, <span class="ruby-value str">'Tt'</span> ) )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>complement (Seq::NA::RNA)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File seq.rb, line 122</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
- <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: SeqError [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">SeqError</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/seq_rb.html">
-
- seq.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- StandardError
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Error class for all exceptions to do with <a href="Seq.html">Seq</a>.
-</p>
-
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Status [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Status</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- Object
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Class for manipulating the execution status of <a
-href="Biopieces.html">Biopieces</a> by setting a status file with a time
-stamp, process id, and command arguments. The status file is used for
-creating log entries and for displaying the runtime status of <a
-href="Biopieces.html">Biopieces</a>.
-</p>
-
- </div>
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000029">delete</a>
-
- <a href="#M000027">get_tmpdir</a>
-
- <a href="#M000028">log</a>
-
- <a href="#M000025">set</a>
-
- <a href="#M000026">set_tmpdir</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Instance methods</h3>
-
-
- <div id="method-M000029" class="method-detail">
- <a name="M000029"></a>
-
- <div class="method-heading">
-
- <a href="Status.src/M000029.html" target="Code" class="method-signature"
- onclick="popupCode('Status.src/M000029.html');return false;">
-
- <span class="method-name">delete</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Delete status file.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000027" class="method-detail">
- <a name="M000027"></a>
-
- <div class="method-heading">
-
- <a href="Status.src/M000027.html" target="Code" class="method-signature"
- onclick="popupCode('Status.src/M000027.html');return false;">
-
- <span class="method-name">get_tmpdir</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Extract the temporary directory path from the status file, and return this
-or nil if not found.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000028" class="method-detail">
- <a name="M000028"></a>
-
- <div class="method-heading">
-
- <a href="Status.src/M000028.html" target="Code" class="method-signature"
- onclick="popupCode('Status.src/M000028.html');return false;">
-
- <span class="method-name">log</span><span class="method-args">(exit_status)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Write the Biopiece status to the log file.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000025" class="method-detail">
- <a name="M000025"></a>
-
- <div class="method-heading">
-
- <a href="Status.src/M000025.html" target="Code" class="method-signature"
- onclick="popupCode('Status.src/M000025.html');return false;">
-
- <span class="method-name">set</span><span class="method-args">()</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Write the status to a status file.
-</p>
-
- </div>
- </div>
-
-
- <div id="method-M000026" class="method-detail">
- <a name="M000026"></a>
-
- <div class="method-heading">
-
- <a href="Status.src/M000026.html" target="Code" class="method-signature"
- onclick="popupCode('Status.src/M000026.html');return false;">
-
- <span class="method-name">set_tmpdir</span><span class="method-args">(tmpdir_path)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Append the a temporary directory path to the status file.
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>set (Status)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 474</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set</span>
- <span class="ruby-identifier">time0</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
-
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-constant">ARGV</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)].<span class="ruby-identifier">join</span>(<span class="ruby-value str">";"</span>)
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>set_tmpdir (Status)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 483</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">tmpdir_path</span>)
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">fh</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">status</span>, <span class="ruby-identifier">tmpdir_path</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">";"</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">"\n"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>get_tmpdir (Status)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 495</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_tmpdir</span>
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
- <span class="ruby-identifier">tmpdir_path</span> = <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>).<span class="ruby-identifier">last</span>
- <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">tmpdir_path</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span>(<span class="ruby-identifier">tmpdir_path</span>)
- <span class="ruby-keyword kw">end</span>
-
- <span class="ruby-keyword kw">nil</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>log (Status)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 505</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">log</span>(<span class="ruby-identifier">exit_status</span>)
- <span class="ruby-identifier">time1</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
- <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
- <span class="ruby-identifier">script</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-identifier">$0</span>)
-
- <span class="ruby-identifier">stream</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>)
- <span class="ruby-identifier">time0</span>, <span class="ruby-identifier">args</span>, <span class="ruby-identifier">tmp_dir</span> = <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>)
- <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">close</span>
-
- <span class="ruby-identifier">elap</span> = <span class="ruby-identifier">time_diff</span>(<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>)
- <span class="ruby-identifier">command</span> = [<span class="ruby-identifier">script</span>, <span class="ruby-identifier">args</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)
- <span class="ruby-identifier">log_file</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_LOG"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/biopieces.log"</span>
-
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">log_file</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"a"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span> <span class="ruby-identifier">file</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>, <span class="ruby-identifier">elap</span>, <span class="ruby-identifier">user</span>, <span class="ruby-identifier">exit_status</span>, <span class="ruby-identifier">command</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\t"</span>) }
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>delete (Status)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 522</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">delete</span>
- <span class="ruby-constant">File</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">path</span>)
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>Class: Stream [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="classHeader">
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Class</strong></td>
- <td class="class-name-in-header">Stream</td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>In:</strong></td>
- <td>
-
-
- <a href="../files/biopieces_rb.html">
-
- biopieces.rb
-
- </a>
-
-
- <br />
-
- </td>
- </tr>
-
-
- <tr class="top-aligned-row">
- <td><strong>Parent:</strong></td>
- <td>
-
- IO
-
- </td>
- </tr>
-
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- </div>
-
-
- <div id="method-list">
- <h3 class="section-bar">Methods</h3>
-
- <div class="name-list">
-
- <a href="#M000030">open</a>
-
- </div>
- </div>
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
- <div id="methods">
-
- <h3 class="section-bar">Public Class methods</h3>
-
-
- <div id="method-M000030" class="method-detail">
- <a name="M000030"></a>
-
- <div class="method-heading">
-
- <a href="Stream.src/M000030.html" target="Code" class="method-signature"
- onclick="popupCode('Stream.src/M000030.html');return false;">
-
- <span class="method-name">open</span><span class="method-args">(options, mode, stdio)</span>
-
- </a>
-
- </div>
-
- <div class="method-description">
-
- <p>
-Open <a href="Biopieces.html">Biopieces</a> output data stream for reading
-from stdin or a file specified in options[“stream_in“] OR
-writing to stdout or a file specified in options[“stream_out“].
-</p>
-
- </div>
- </div>
-
-
-
- </div>
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>open (Stream)</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-</head>
-<body class="standalone-code">
- <pre><span class="ruby-comment cmt"># File biopieces.rb, line 547</span>
- <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">options</span>, <span class="ruby-identifier">mode</span>, <span class="ruby-identifier">stdio</span>)
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"r"</span>
- <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span> <span class="ruby-value">? </span><span class="ruby-identifier">read</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value str">"stream_in"</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"w"</span>
- <span class="ruby-identifier">options</span>[<span class="ruby-value str">"stream_out"</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value str">"stream_out"</span>], <span class="ruby-identifier">options</span>[<span class="ruby-value str">"compress"</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
- <span class="ruby-keyword kw">else</span>
- <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad mode #{mode}"</span>
- <span class="ruby-keyword kw">end</span>
- <span class="ruby-keyword kw">end</span></pre>
-</body>
-</html>
+++ /dev/null
-Sat, 19 Mar 2011 16:29:12 +0100
-./base36.rb Fri, 11 Feb 2011 19:42:32 +0100
-./biopieces.rb Sat, 19 Mar 2011 09:14:44 +0100
-./bitarray.rb Thu, 17 Mar 2011 15:02:03 +0100
-./bits.rb Tue, 08 Mar 2011 11:37:57 +0100
-./boulder.rb Sat, 19 Mar 2011 09:17:13 +0100
-./digest.rb Sat, 19 Mar 2011 15:41:06 +0100
-./fasta.rb Sat, 19 Mar 2011 09:11:06 +0100
-./fastq.rb Sat, 19 Mar 2011 09:09:52 +0100
-./filesys.rb Fri, 18 Mar 2011 22:13:22 +0100
-./genbank.rb Sat, 19 Mar 2011 09:19:25 +0100
-./seq.rb Sat, 19 Mar 2011 16:29:08 +0100
-./sff.rb Fri, 11 Feb 2011 19:55:38 +0100
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: digest.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-03-19 15:41:06 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>seq</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: fasta.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-03-19 09:11:06 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>seq</li>
-
- <li>filesys</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: fastq.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-03-19 09:09:52 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>seq</li>
-
- <li>filesys</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>File: biopieces.rb [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="fileHeader">
- <h1>biopieces.rb</h1>
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Path:</strong></td>
- <td>biopieces.rb
-
- </td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>Last Update:</strong></td>
- <td>2010-08-17 14:23:28 +0200</td>
- </tr>
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-Copyright (C) 2007-2010 Martin A. Hansen.
-</p>
-
- </div>
-
- <div id="requires-list">
- <h3 class="section-bar">Required files</h3>
-
- <div class="name-list">
-
- fileutils
-
- date
-
- optparse
-
- open3
-
- pp
-
- </div>
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>File: fasta.rb [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="fileHeader">
- <h1>fasta.rb</h1>
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Path:</strong></td>
- <td>fasta.rb
-
- </td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>Last Update:</strong></td>
- <td>2010-08-18 21:33:24 +0200</td>
- </tr>
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- <div id="description">
- <p>
-This program is free software; you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation; either version 2 of the License, or (at your option)
-any later version.
-</p>
-
- </div>
-
- <div id="requires-list">
- <h3 class="section-bar">Required files</h3>
-
- <div class="name-list">
-
- seq
-
- zlib
-
- </div>
- </div>
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
-"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <title>File: seq.rb [RDoc Documentation]</title>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <meta http-equiv="Content-Script-Type" content="text/javascript" />
- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
- <script type="text/javascript">
- // <![CDATA[
-
- function popupCode( url ) {
- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
- }
-
- function toggleCode( id ) {
- if ( document.getElementById )
- elem = document.getElementById( id );
- else if ( document.all )
- elem = eval( "document.all." + id );
- else
- return false;
-
- elemStyle = elem.style;
-
- if ( elemStyle.display != "block" ) {
- elemStyle.display = "block"
- } else {
- elemStyle.display = "none"
- }
-
- return true;
- }
-
- // Make codeblocks hidden by default
- document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }<\/style>" )
-
- // ]]>
- </script>
-
-</head>
-<body>
-
-
- <div id="fileHeader">
- <h1>seq.rb</h1>
- <table class="header-table">
- <tr class="top-aligned-row">
- <td><strong>Path:</strong></td>
- <td>seq.rb
-
- </td>
- </tr>
- <tr class="top-aligned-row">
- <td><strong>Last Update:</strong></td>
- <td>2010-08-17 08:33:38 +0200</td>
- </tr>
- </table>
- </div>
- <!-- banner header -->
-
- <div id="bodyContent">
-
- <div id="contextContent">
-
- </div>
-
-
- </div>
-
- <!-- if includes -->
-
- <div id="section">
-
- <div id="constants-list">
- <h3 class="section-bar">Constants</h3>
-
- <div class="name-list">
- <table summary="Constants">
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">DNA</td>
- <td>=</td>
- <td class="context-item-value">%w[a t c g]</td>
-
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">RNA</td>
- <td>=</td>
- <td class="context-item-value">%w[a u c g]</td>
-
- </tr>
-
- <tr class="top-aligned-row context-row">
- <td class="context-item-name">PROTEIN</td>
- <td>=</td>
- <td class="context-item-value">%w[f l s y c w p h q r i m t n k v a d e g]</td>
-
- </tr>
-
- </table>
- </div>
- </div>
-
-
-
-
- <!-- if method_list -->
-
-
-
-
- </div>
-
-<div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: filesys.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
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+++ /dev/null
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-
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- <li><a href="BitArray.html#method-i-bits_on">#bits_on — BitArray</a></li>
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-
- <li><a href="Casts.html#method-i-check_keys">#check_keys — Casts</a></li>
-
- <li><a href="SFF.html#method-i-check_magic_number">#check_magic_number — SFF</a></li>
-
- <li><a href="Casts.html#method-i-check_val_allowed">#check_val_allowed — Casts</a></li>
-
- <li><a href="Casts.html#method-i-check_val_default">#check_val_default — Casts</a></li>
-
- <li><a href="Casts.html#method-i-check_val_disallowed">#check_val_disallowed — Casts</a></li>
-
- <li><a href="Casts.html#method-i-check_val_long">#check_val_long — Casts</a></li>
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- <li><a href="Casts.html#method-i-check_val_short">#check_val_short — Casts</a></li>
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-
- <li><a href="Casts.html#method-i-check_values">#check_values — Casts</a></li>
-
- <li><a href="SFF.html#method-i-check_version">#check_version — SFF</a></li>
-
- <li><a href="Read.html#method-i-clip">#clip — Read</a></li>
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-
- <li><a href="Seq.html#method-i-complement">#complement — Seq</a></li>
-
- <li><a href="Seq.html#method-i-composition">#composition — Seq</a></li>
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- <li><a href="Seq.html#method-i-convert_solexa2illumina%21">#convert_solexa2illumina! — Seq</a></li>
-
- <li><a href="Read.html#method-i-coordinates_get">#coordinates_get — Read</a></li>
-
- <li><a href="Status.html#method-i-delete">#delete — Status</a></li>
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-
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-
- <li><a href="GenbankFeatures.html#method-i-each">#each — GenbankFeatures</a></li>
-
- <li><a href="Genbank.html#method-i-each">#each — Genbank</a></li>
-
- <li><a href="Digest.html#method-i-each">#each — Digest</a></li>
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-
- <li><a href="Biopieces.html#method-i-each_record">#each_record — Biopieces</a></li>
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-
- <li><a href="Fasta.html#method-i-get_entry">#get_entry — Fasta</a></li>
-
- <li><a href="Fastq.html#method-i-get_entry">#get_entry — Fastq</a></li>
-
- <li><a href="Genbank.html#method-i-get_entry">#get_entry — Genbank</a></li>
-
- <li><a href="Genbank.html#method-i-get_keys">#get_keys — Genbank</a></li>
-
- <li><a href="GenbankFeatures.html#method-i-get_quals">#get_quals — GenbankFeatures</a></li>
-
- <li><a href="Genbank.html#method-i-get_seq">#get_seq — Genbank</a></li>
-
- <li><a href="Status.html#method-i-get_tmpdir">#get_tmpdir — Status</a></li>
-
- <li><a href="Seq.html#method-i-hard_mask">#hard_mask — Seq</a></li>
-
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-
- <li><a href="Seq.html#method-i-homopol_max">#homopol_max — Seq</a></li>
-
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-
- <li><a href="Seq.html#method-i-is_protein%3F">#is_protein? — Seq</a></li>
-
- <li><a href="Seq.html#method-i-is_rna%3F">#is_rna? — Seq</a></li>
-
- <li><a href="Seq.html#method-i-len">#len — Seq</a></li>
-
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-
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-
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-
- <li><a href="Read.html#method-i-mask">#mask — Read</a></li>
-
- <li><a href="Seq.html#method-i-match">#match — Seq</a></li>
-
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-
- <li><a href="OptionHandler.html#method-i-options_check">#options_check — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_allowed">#options_check_allowed — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_dir">#options_check_dir — OptionHandler</a></li>
-
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-
- <li><a href="OptionHandler.html#method-i-options_check_file">#options_check_file — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_files">#options_check_files — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_int">#options_check_int — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_mandatory">#options_check_mandatory — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_check_uint">#options_check_uint — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_default">#options_default — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_glob">#options_glob — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-options_parse">#options_parse — OptionHandler</a></li>
-
- <li><a href="Biopieces.html#method-i-parse">#parse — Biopieces</a></li>
-
- <li><a href="Locator.html#method-i-parse_locator">#parse_locator — Locator</a></li>
-
- <li><a href="Status.html#method-i-path">#path — Status</a></li>
-
- <li><a href="OptionHandler.html#method-i-print_usage_and_exit">#print_usage_and_exit — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-print_usage_full%3F">#print_usage_full? — OptionHandler</a></li>
-
- <li><a href="OptionHandler.html#method-i-print_usage_short%3F">#print_usage_short? — OptionHandler</a></li>
-
- <li><a href="Fasta.html#method-i-puts">#puts — Fasta</a></li>
-
- <li><a href="Fastq.html#method-i-puts">#puts — Fastq</a></li>
-
- <li><a href="Biopieces.html#method-i-puts">#puts — Biopieces</a></li>
-
- <li><a href="SFF.html#method-i-read_parse">#read_parse — SFF</a></li>
-
- <li><a href="Seq.html#method-i-revcomp">#revcomp — Seq</a></li>
-
- <li><a href="Seq.html#method-i-reverse">#reverse — Seq</a></li>
-
- <li><a href="Seq.html#method-i-reverse_complement">#reverse_complement — Seq</a></li>
-
- <li><a href="Locator.html#method-i-s_beg">#s_beg — Locator</a></li>
-
- <li><a href="Locator.html#method-i-s_end">#s_end — Locator</a></li>
-
- <li><a href="Status.html#method-i-set">#set — Status</a></li>
-
- <li><a href="Status.html#method-i-set_tmpdir">#set_tmpdir — Status</a></li>
-
- <li><a href="Seq.html#method-i-soft_mask">#soft_mask — Seq</a></li>
-
- <li><a href="Seq.html#method-i-solexa2phred">#solexa2phred — Seq</a></li>
-
- <li><a href="Seq.html#method-i-solexa_char2illumina_char">#solexa_char2illumina_char — Seq</a></li>
-
- <li><a href="Locator.html#method-i-strand">#strand — Locator</a></li>
-
- <li><a href="Seq.html#method-i-subseq">#subseq — Seq</a></li>
-
- <li><a href="Seq.html#method-i-subseq%21">#subseq! — Seq</a></li>
-
- <li><a href="Seq.html#method-i-subseq_rand">#subseq_rand — Seq</a></li>
-
- <li><a href="Status.html#method-i-time_diff">#time_diff — Status</a></li>
-
- <li><a href="Boulder.html#method-i-to_boulder">#to_boulder — Boulder</a></li>
-
- <li><a href="Seq.html#method-i-to_bp">#to_bp — Seq</a></li>
-
- <li><a href="Read.html#method-i-to_bp">#to_bp — Read</a></li>
-
- <li><a href="Seq.html#method-i-to_dna">#to_dna — Seq</a></li>
-
- <li><a href="Seq.html#method-i-to_fasta">#to_fasta — Seq</a></li>
-
- <li><a href="Seq.html#method-i-to_key">#to_key — Seq</a></li>
-
- <li><a href="Seq.html#method-i-to_rna">#to_rna — Seq</a></li>
-
- <li><a href="BitArray.html#method-i-to_s">#to_s — BitArray</a></li>
-
- <li><a href="Biopieces.html#method-i-to_s">#to_s — Biopieces</a></li>
-
- <li><a href="Casts.html#method-i-ubiquitous">#ubiquitous — Casts</a></li>
-
- <li><a href="GenbankFeatures.html#method-i-want_feat%3F">#want_feat? — GenbankFeatures</a></li>
-
- <li><a href="Genbank.html#method-i-want_key%3F">#want_key? — Genbank</a></li>
-
- <li><a href="GenbankFeatures.html#method-i-want_qual%3F">#want_qual? — GenbankFeatures</a></li>
-
- <li><a href="OptionHandler.html#method-i-wiki_path">#wiki_path — OptionHandler</a></li>
-
- <li><a href="BitArray.html#method-i-%7C">#| — BitArray</a></li>
-
- <li><a href="String.html#method-i-%7C">#| — String</a></li>
-
- </ul>
-
- <div id="validator-badges">
- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
- <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
- Rdoc Generator</a> 1.1.6</small>.</p>
- </div>
-</body>
-</html>
+++ /dev/null
-/**
- *
- * Darkfish Page Functions
- * $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
- *
- * Author: Michael Granger <mgranger@laika.com>
- *
- */
-
-/* Provide console simulation for firebug-less environments */
-if (!("console" in window) || !("firebug" in console)) {
- var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
- "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
-
- window.console = {};
- for (var i = 0; i < names.length; ++i)
- window.console[names[i]] = function() {};
-};
-
-
-/**
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- */
-$.fn.unwrap = function( expr ) {
- return this.each( function() {
- $(this).parents( expr ).eq( 0 ).after( this ).remove();
- });
-};
-
-
-function showSource( e ) {
- var target = e.target;
- var codeSections = $(target).
- parents('.method-detail').
- find('.method-source-code');
-
- $(target).
- parents('.method-detail').
- find('.method-source-code').
- slideToggle();
-};
-
-function hookSourceViews() {
- $('.method-description,.method-heading').click( showSource );
-};
-
-function toggleDebuggingSection() {
- $('.debugging-section').slideToggle();
-};
-
-function hookDebuggingToggle() {
- $('#debugging-toggle img').click( toggleDebuggingSection );
-};
-
-function hookQuickSearch() {
- $('.quicksearch-field').each( function() {
- var searchElems = $(this).parents('.section').find( 'li' );
- var toggle = $(this).parents('.section').find('h3 .search-toggle');
- // console.debug( "Toggle is: %o", toggle );
- var qsbox = $(this).parents('form').get( 0 );
-
- $(this).quicksearch( this, searchElems, {
- noSearchResultsIndicator: 'no-class-search-results',
- focusOnLoad: false
- });
- $(toggle).click( function() {
- // console.debug( "Toggling qsbox: %o", qsbox );
- $(qsbox).toggle();
- });
- });
-};
-
-function highlightTarget( anchor ) {
- console.debug( "Highlighting target '%s'.", anchor );
-
- $("a[name=" + anchor + "]").each( function() {
- if ( !$(this).parent().parent().hasClass('target-section') ) {
- console.debug( "Wrapping the target-section" );
- $('div.method-detail').unwrap( 'div.target-section' );
- $(this).parent().wrap( '<div class="target-section"></div>' );
- } else {
- console.debug( "Already wrapped." );
- }
- });
-};
-
-function highlightLocationTarget() {
- console.debug( "Location hash: %s", window.location.hash );
- if ( ! window.location.hash || window.location.hash.length == 0 ) return;
-
- var anchor = window.location.hash.substring(1);
- console.debug( "Found anchor: %s; matching %s", anchor, "a[name=" + anchor + "]" );
-
- highlightTarget( anchor );
-};
-
-function highlightClickTarget( event ) {
- console.debug( "Highlighting click target for event %o", event.target );
- try {
- var anchor = $(event.target).attr( 'href' ).substring(1);
- console.debug( "Found target anchor: %s", anchor );
- highlightTarget( anchor );
- } catch ( err ) {
- console.error( "Exception while highlighting: %o", err );
- };
-};
-
-
-$(document).ready( function() {
- hookSourceViews();
- hookDebuggingToggle();
- hookQuickSearch();
- highlightLocationTarget();
-
- $('ul.link-list a').bind( "click", highlightClickTarget );
-});
+++ /dev/null
-/*
- * jQuery 1.2.6 - New Wave Javascript
- *
- * Copyright (c) 2008 John Resig (jquery.com)
- * Dual licensed under the MIT (MIT-LICENSE.txt)
- * and GPL (GPL-LICENSE.txt) licenses.
- *
- * $Date: 2008-09-25 09:50:52 -0700 (Thu, 25 Sep 2008) $
- * $Rev: 38 $
- */
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ret=s.url.replace(/(\?|&)_=.*?(&|$)/,"$1_="+ts+"$2");s.url=ret+((ret==s.url)?(s.url.match(/\?/)?"&":"?")+"_="+ts:"");}if(s.data&&type=="GET"){s.url+=(s.url.match(/\?/)?"&":"?")+s.data;s.data=null;}if(s.global&&!jQuery.active++)jQuery.event.trigger("ajaxStart");var remote=/^(?:\w+:)?\/\/([^\/?#]+)/;if(s.dataType=="script"&&type=="GET"&&remote.test(s.url)&&remote.exec(s.url)[1]!=location.host){var head=document.getElementsByTagName("head")[0];var script=document.createElement("script");script.src=s.url;if(s.scriptCharset)script.charset=s.scriptCharset;if(!jsonp){var done=false;script.onload=script.onreadystatechange=function(){if(!done&&(!this.readyState||this.readyState=="loaded"||this.readyState=="complete")){done=true;success();complete();head.removeChild(script);}};}head.appendChild(script);return undefined;}var requestDone=false;var xhr=window.ActiveXObject?new ActiveXObject("Microsoft.XMLHTTP"):new XMLHttpRequest();if(s.username)xhr.open(type,s.url,s.async,s.username,s.password);else
-xhr.open(type,s.url,s.async);try{if(s.data)xhr.setRequestHeader("Content-Type",s.contentType);if(s.ifModified)xhr.setRequestHeader("If-Modified-Since",jQuery.lastModified[s.url]||"Thu, 01 Jan 1970 00:00:00 GMT");xhr.setRequestHeader("X-Requested-With","XMLHttpRequest");xhr.setRequestHeader("Accept",s.dataType&&s.accepts[s.dataType]?s.accepts[s.dataType]+", */*":s.accepts._default);}catch(e){}if(s.beforeSend&&s.beforeSend(xhr,s)===false){s.global&&jQuery.active--;xhr.abort();return false;}if(s.global)jQuery.event.trigger("ajaxSend",[xhr,s]);var onreadystatechange=function(isTimeout){if(!requestDone&&xhr&&(xhr.readyState==4||isTimeout=="timeout")){requestDone=true;if(ival){clearInterval(ival);ival=null;}status=isTimeout=="timeout"&&"timeout"||!jQuery.httpSuccess(xhr)&&"error"||s.ifModified&&jQuery.httpNotModified(xhr,s.url)&&"notmodified"||"success";if(status=="success"){try{data=jQuery.httpData(xhr,s.dataType,s.dataFilter);}catch(e){status="parsererror";}}if(status=="success"){var modRes;try{modRes=xhr.getResponseHeader("Last-Modified");}catch(e){}if(s.ifModified&&modRes)jQuery.lastModified[s.url]=modRes;if(!jsonp)success();}else
-jQuery.handleError(s,xhr,status);complete();if(s.async)xhr=null;}};if(s.async){var ival=setInterval(onreadystatechange,13);if(s.timeout>0)setTimeout(function(){if(xhr){xhr.abort();if(!requestDone)onreadystatechange("timeout");}},s.timeout);}try{xhr.send(s.data);}catch(e){jQuery.handleError(s,xhr,null,e);}if(!s.async)onreadystatechange();function success(){if(s.success)s.success(data,status);if(s.global)jQuery.event.trigger("ajaxSuccess",[xhr,s]);}function complete(){if(s.complete)s.complete(xhr,status);if(s.global)jQuery.event.trigger("ajaxComplete",[xhr,s]);if(s.global&&!--jQuery.active)jQuery.event.trigger("ajaxStop");}return xhr;},handleError:function(s,xhr,status,e){if(s.error)s.error(xhr,status,e);if(s.global)jQuery.event.trigger("ajaxError",[xhr,s,e]);},active:0,httpSuccess:function(xhr){try{return!xhr.status&&location.protocol=="file:"||(xhr.status>=200&&xhr.status<300)||xhr.status==304||xhr.status==1223||jQuery.browser.safari&&xhr.status==undefined;}catch(e){}return false;},httpNotModified:function(xhr,url){try{var xhrRes=xhr.getResponseHeader("Last-Modified");return xhr.status==304||xhrRes==jQuery.lastModified[url]||jQuery.browser.safari&&xhr.status==undefined;}catch(e){}return false;},httpData:function(xhr,type,filter){var ct=xhr.getResponseHeader("content-type"),xml=type=="xml"||!type&&ct&&ct.indexOf("xml")>=0,data=xml?xhr.responseXML:xhr.responseText;if(xml&&data.documentElement.tagName=="parsererror")throw"parsererror";if(filter)data=filter(data,type);if(type=="script")jQuery.globalEval(data);if(type=="json")data=eval("("+data+")");return data;},param:function(a){var s=[];if(a.constructor==Array||a.jquery)jQuery.each(a,function(){s.push(encodeURIComponent(this.name)+"="+encodeURIComponent(this.value));});else
-for(var j in a)if(a[j]&&a[j].constructor==Array)jQuery.each(a[j],function(){s.push(encodeURIComponent(j)+"="+encodeURIComponent(this));});else
-s.push(encodeURIComponent(j)+"="+encodeURIComponent(jQuery.isFunction(a[j])?a[j]():a[j]));return s.join("&").replace(/%20/g,"+");}});jQuery.fn.extend({show:function(speed,callback){return speed?this.animate({height:"show",width:"show",opacity:"show"},speed,callback):this.filter(":hidden").each(function(){this.style.display=this.oldblock||"";if(jQuery.css(this,"display")=="none"){var elem=jQuery("<"+this.tagName+" />").appendTo("body");this.style.display=elem.css("display");if(this.style.display=="none")this.style.display="block";elem.remove();}}).end();},hide:function(speed,callback){return speed?this.animate({height:"hide",width:"hide",opacity:"hide"},speed,callback):this.filter(":visible").each(function(){this.oldblock=this.oldblock||jQuery.css(this,"display");this.style.display="none";}).end();},_toggle:jQuery.fn.toggle,toggle:function(fn,fn2){return jQuery.isFunction(fn)&&jQuery.isFunction(fn2)?this._toggle.apply(this,arguments):fn?this.animate({height:"toggle",width:"toggle",opacity:"toggle"},fn,fn2):this.each(function(){jQuery(this)[jQuery(this).is(":hidden")?"show":"hide"]();});},slideDown:function(speed,callback){return this.animate({height:"show"},speed,callback);},slideUp:function(speed,callback){return this.animate({height:"hide"},speed,callback);},slideToggle:function(speed,callback){return this.animate({height:"toggle"},speed,callback);},fadeIn:function(speed,callback){return this.animate({opacity:"show"},speed,callback);},fadeOut:function(speed,callback){return this.animate({opacity:"hide"},speed,callback);},fadeTo:function(speed,to,callback){return this.animate({opacity:to},speed,callback);},animate:function(prop,speed,easing,callback){var optall=jQuery.speed(speed,easing,callback);return this[optall.queue===false?"each":"queue"](function(){if(this.nodeType!=1)return false;var opt=jQuery.extend({},optall),p,hidden=jQuery(this).is(":hidden"),self=this;for(p in prop){if(prop[p]=="hide"&&hidden||prop[p]=="show"&&!hidden)return opt.complete.call(this);if(p=="height"||p=="width"){opt.display=jQuery.css(this,"display");opt.overflow=this.style.overflow;}}if(opt.overflow!=null)this.style.overflow="hidden";opt.curAnim=jQuery.extend({},prop);jQuery.each(prop,function(name,val){var e=new jQuery.fx(self,opt,name);if(/toggle|show|hide/.test(val))e[val=="toggle"?hidden?"show":"hide":val](prop);else{var parts=val.toString().match(/^([+-]=)?([\d+-.]+)(.*)$/),start=e.cur(true)||0;if(parts){var end=parseFloat(parts[2]),unit=parts[3]||"px";if(unit!="px"){self.style[name]=(end||1)+unit;start=((end||1)/e.cur(true))*start;self.style[name]=start+unit;}if(parts[1])end=((parts[1]=="-="?-1:1)*end)+start;e.custom(start,end,unit);}else
-e.custom(start,val,"");}});return true;});},queue:function(type,fn){if(jQuery.isFunction(type)||(type&&type.constructor==Array)){fn=type;type="fx";}if(!type||(typeof type=="string"&&!fn))return queue(this[0],type);return this.each(function(){if(fn.constructor==Array)queue(this,type,fn);else{queue(this,type).push(fn);if(queue(this,type).length==1)fn.call(this);}});},stop:function(clearQueue,gotoEnd){var timers=jQuery.timers;if(clearQueue)this.queue([]);this.each(function(){for(var i=timers.length-1;i>=0;i--)if(timers[i].elem==this){if(gotoEnd)timers[i](true);timers.splice(i,1);}});if(!gotoEnd)this.dequeue();return this;}});var queue=function(elem,type,array){if(elem){type=type||"fx";var q=jQuery.data(elem,type+"queue");if(!q||array)q=jQuery.data(elem,type+"queue",jQuery.makeArray(array));}return q;};jQuery.fn.dequeue=function(type){type=type||"fx";return this.each(function(){var q=queue(this,type);q.shift();if(q.length)q[0].call(this);});};jQuery.extend({speed:function(speed,easing,fn){var opt=speed&&speed.constructor==Object?speed:{complete:fn||!fn&&easing||jQuery.isFunction(speed)&&speed,duration:speed,easing:fn&&easing||easing&&easing.constructor!=Function&&easing};opt.duration=(opt.duration&&opt.duration.constructor==Number?opt.duration:jQuery.fx.speeds[opt.duration])||jQuery.fx.speeds.def;opt.old=opt.complete;opt.complete=function(){if(opt.queue!==false)jQuery(this).dequeue();if(jQuery.isFunction(opt.old))opt.old.call(this);};return opt;},easing:{linear:function(p,n,firstNum,diff){return firstNum+diff*p;},swing:function(p,n,firstNum,diff){return((-Math.cos(p*Math.PI)/2)+0.5)*diff+firstNum;}},timers:[],timerId:null,fx:function(elem,options,prop){this.options=options;this.elem=elem;this.prop=prop;if(!options.orig)options.orig={};}});jQuery.fx.prototype={update:function(){if(this.options.step)this.options.step.call(this.elem,this.now,this);(jQuery.fx.step[this.prop]||jQuery.fx.step._default)(this);if(this.prop=="height"||this.prop=="width")this.elem.style.display="block";},cur:function(force){if(this.elem[this.prop]!=null&&this.elem.style[this.prop]==null)return this.elem[this.prop];var r=parseFloat(jQuery.css(this.elem,this.prop,force));return r&&r>-10000?r:parseFloat(jQuery.curCSS(this.elem,this.prop))||0;},custom:function(from,to,unit){this.startTime=now();this.start=from;this.end=to;this.unit=unit||this.unit||"px";this.now=this.start;this.pos=this.state=0;this.update();var self=this;function t(gotoEnd){return self.step(gotoEnd);}t.elem=this.elem;jQuery.timers.push(t);if(jQuery.timerId==null){jQuery.timerId=setInterval(function(){var timers=jQuery.timers;for(var i=0;i<timers.length;i++)if(!timers[i]())timers.splice(i--,1);if(!timers.length){clearInterval(jQuery.timerId);jQuery.timerId=null;}},13);}},show:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.show=true;this.custom(0,this.cur());if(this.prop=="width"||this.prop=="height")this.elem.style[this.prop]="1px";jQuery(this.elem).show();},hide:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.hide=true;this.custom(this.cur(),0);},step:function(gotoEnd){var t=now();if(gotoEnd||t>this.options.duration+this.startTime){this.now=this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;var done=true;for(var i in this.options.curAnim)if(this.options.curAnim[i]!==true)done=false;if(done){if(this.options.display!=null){this.elem.style.overflow=this.options.overflow;this.elem.style.display=this.options.display;if(jQuery.css(this.elem,"display")=="none")this.elem.style.display="block";}if(this.options.hide)this.elem.style.display="none";if(this.options.hide||this.options.show)for(var p in this.options.curAnim)jQuery.attr(this.elem.style,p,this.options.orig[p]);}if(done)this.options.complete.call(this.elem);return false;}else{var n=t-this.startTime;this.state=n/this.options.duration;this.pos=jQuery.easing[this.options.easing||(jQuery.easing.swing?"swing":"linear")](this.state,n,0,1,this.options.duration);this.now=this.start+((this.end-this.start)*this.pos);this.update();}return true;}};jQuery.extend(jQuery.fx,{speeds:{slow:600,fast:200,def:400},step:{scrollLeft:function(fx){fx.elem.scrollLeft=fx.now;},scrollTop:function(fx){fx.elem.scrollTop=fx.now;},opacity:function(fx){jQuery.attr(fx.elem.style,"opacity",fx.now);},_default:function(fx){fx.elem.style[fx.prop]=fx.now+fx.unit;}}});jQuery.fn.offset=function(){var left=0,top=0,elem=this[0],results;if(elem)with(jQuery.browser){var parent=elem.parentNode,offsetChild=elem,offsetParent=elem.offsetParent,doc=elem.ownerDocument,safari2=safari&&parseInt(version)<522&&!/adobeair/i.test(userAgent),css=jQuery.curCSS,fixed=css(elem,"position")=="fixed";if(elem.getBoundingClientRect){var box=elem.getBoundingClientRect();add(box.left+Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),box.top+Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));add(-doc.documentElement.clientLeft,-doc.documentElement.clientTop);}else{add(elem.offsetLeft,elem.offsetTop);while(offsetParent){add(offsetParent.offsetLeft,offsetParent.offsetTop);if(mozilla&&!/^t(able|d|h)$/i.test(offsetParent.tagName)||safari&&!safari2)border(offsetParent);if(!fixed&&css(offsetParent,"position")=="fixed")fixed=true;offsetChild=/^body$/i.test(offsetParent.tagName)?offsetChild:offsetParent;offsetParent=offsetParent.offsetParent;}while(parent&&parent.tagName&&!/^body|html$/i.test(parent.tagName)){if(!/^inline|table.*$/i.test(css(parent,"display")))add(-parent.scrollLeft,-parent.scrollTop);if(mozilla&&css(parent,"overflow")!="visible")border(parent);parent=parent.parentNode;}if((safari2&&(fixed||css(offsetChild,"position")=="absolute"))||(mozilla&&css(offsetChild,"position")!="absolute"))add(-doc.body.offsetLeft,-doc.body.offsetTop);if(fixed)add(Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));}results={top:top,left:left};}function border(elem){add(jQuery.curCSS(elem,"borderLeftWidth",true),jQuery.curCSS(elem,"borderTopWidth",true));}function add(l,t){left+=parseInt(l,10)||0;top+=parseInt(t,10)||0;}return results;};jQuery.fn.extend({position:function(){var left=0,top=0,results;if(this[0]){var offsetParent=this.offsetParent(),offset=this.offset(),parentOffset=/^body|html$/i.test(offsetParent[0].tagName)?{top:0,left:0}:offsetParent.offset();offset.top-=num(this,'marginTop');offset.left-=num(this,'marginLeft');parentOffset.top+=num(offsetParent,'borderTopWidth');parentOffset.left+=num(offsetParent,'borderLeftWidth');results={top:offset.top-parentOffset.top,left:offset.left-parentOffset.left};}return results;},offsetParent:function(){var offsetParent=this[0].offsetParent;while(offsetParent&&(!/^body|html$/i.test(offsetParent.tagName)&&jQuery.css(offsetParent,'position')=='static'))offsetParent=offsetParent.offsetParent;return jQuery(offsetParent);}});jQuery.each(['Left','Top'],function(i,name){var method='scroll'+name;jQuery.fn[method]=function(val){if(!this[0])return;return val!=undefined?this.each(function(){this==window||this==document?window.scrollTo(!i?val:jQuery(window).scrollLeft(),i?val:jQuery(window).scrollTop()):this[method]=val;}):this[0]==window||this[0]==document?self[i?'pageYOffset':'pageXOffset']||jQuery.boxModel&&document.documentElement[method]||document.body[method]:this[0][method];};});jQuery.each(["Height","Width"],function(i,name){var tl=i?"Left":"Top",br=i?"Right":"Bottom";jQuery.fn["inner"+name]=function(){return this[name.toLowerCase()]()+num(this,"padding"+tl)+num(this,"padding"+br);};jQuery.fn["outer"+name]=function(margin){return this["inner"+name]()+num(this,"border"+tl+"Width")+num(this,"border"+br+"Width")+(margin?num(this,"margin"+tl)+num(this,"margin"+br):0);};});})();
\ No newline at end of file
+++ /dev/null
-/**
- *
- * JQuery QuickSearch - Hook up a form field to hide non-matching elements.
- * $Id: quicksearch.js 53 2009-01-07 02:52:03Z deveiant $
- *
- * Author: Michael Granger <mgranger@laika.com>
- *
- */
-jQuery.fn.quicksearch = function( target, searchElems, options ) {
- // console.debug( "Quicksearch fn" );
-
- var settings = {
- delay: 250,
- clearButton: false,
- highlightMatches: false,
- focusOnLoad: false,
- noSearchResultsIndicator: null
- };
- if ( options ) $.extend( settings, options );
-
- return jQuery(this).each( function() {
- // console.debug( "Creating a new quicksearch on %o for %o", this, searchElems );
- new jQuery.quicksearch( this, searchElems, settings );
- });
-};
-
-
-jQuery.quicksearch = function( searchBox, searchElems, settings ) {
- var timeout;
- var boxdiv = $(searchBox).parents('div').eq(0);
-
- function init() {
- setupKeyEventHandlers();
- focusOnLoad();
- };
-
- function setupKeyEventHandlers() {
- // console.debug( "Hooking up the 'keypress' event to %o", searchBox );
- $(searchBox).
- unbind( 'keyup' ).
- keyup( function(e) { return onSearchKey( e.keyCode ); });
- $(searchBox).
- unbind( 'keypress' ).
- keypress( function(e) {
- switch( e.which ) {
- // Execute the search on Enter, Tab, or Newline
- case 9:
- case 13:
- case 10:
- clearTimeout( timeout );
- e.preventDefault();
- doQuickSearch();
- break;
-
- // Allow backspace
- case 8:
- return true;
- break;
-
- // Only allow valid search characters
- default:
- return validQSChar( e.charCode );
- }
- });
- };
-
- function focusOnLoad() {
- if ( !settings.focusOnLoad ) return false;
- $(searchBox).focus();
- };
-
- function onSearchKey ( code ) {
- clearTimeout( timeout );
- // console.debug( "...scheduling search." );
- timeout = setTimeout( doQuickSearch, settings.delay );
- };
-
- function validQSChar( code ) {
- var c = String.fromCharCode( code );
- return (
- (c == ':') ||
- (c >= 'a' && c <= 'z') ||
- (c >= 'A' && c <= 'Z')
- );
- };
-
- function doQuickSearch() {
- var searchText = searchBox.value;
- var pat = new RegExp( searchText, "im" );
- var shownCount = 0;
-
- if ( settings.noSearchResultsIndicator ) {
- $('#' + settings.noSearchResultsIndicator).hide();
- }
-
- // All elements start out hidden
- $(searchElems).each( function(index) {
- var str = $(this).text();
-
- if ( pat.test(str) ) {
- shownCount += 1;
- $(this).fadeIn();
- } else {
- $(this).hide();
- }
- });
-
- if ( shownCount == 0 && settings.noSearchResultsIndicator ) {
- $('#' + settings.noSearchResultsIndicator).slideDown();
- }
- };
-
- init();
-};
+++ /dev/null
-/*
- * Thickbox 3 - One Box To Rule Them All.
- * By Cody Lindley (http://www.codylindley.com)
- * Copyright (c) 2007 cody lindley
- * Licensed under the MIT License: http://www.opensource.org/licenses/mit-license.php
-*/
-
-var tb_pathToImage = "../images/loadingAnimation.gif";
-
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-.file-popup dl {
- font-size: 80%;
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- background-color: #dedede;
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-.file dt {
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- -moz-border-radius: 3px;
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-
-
-
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-#TB_window {
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-#TB_window :link,
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-#TB_window :link:hover,
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-#TB_window :link:active,
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-#TB_window :link:focus,
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-#TB_overlay {
- position: fixed;
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- top: 0px;
- left: 0px;
- height:100%;
- width:100%;
-}
-
-.TB_overlayMacFFBGHack {background: url(images/macFFBgHack.png) repeat;}
-.TB_overlayBG {
- background-color:#000;
- filter:alpha(opacity=75);
- -moz-opacity: 0.75;
- opacity: 0.75;
-}
-
-* html #TB_overlay { /* ie6 hack */
- position: absolute;
- height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px');
-}
-
-#TB_window {
- position: fixed;
- background: #ffffff;
- z-index: 102;
- color:#000000;
- display:none;
- border: 4px solid #525252;
- text-align:left;
- top:50%;
- left:50%;
-}
-
-* html #TB_window { /* ie6 hack */
-position: absolute;
-margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px');
-}
-
-#TB_window img#TB_Image {
- display:block;
- margin: 15px 0 0 15px;
- border-right: 1px solid #ccc;
- border-bottom: 1px solid #ccc;
- border-top: 1px solid #666;
- border-left: 1px solid #666;
-}
-
-#TB_caption{
- height:25px;
- padding:7px 30px 10px 25px;
- float:left;
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-
-#TB_closeWindow{
- height:25px;
- padding:11px 25px 10px 0;
- float:right;
-}
-
-#TB_closeAjaxWindow{
- padding:7px 10px 5px 0;
- margin-bottom:1px;
- text-align:right;
- float:right;
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- float:left;
- padding:7px 0 5px 10px;
- margin-bottom:1px;
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- color: #dedede;
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- margin: -6px 0 0 -104px; /* -height/2 0 0 -width/2 */
-}
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-* html #TB_load { /* ie6 hack */
-position: absolute;
-margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px');
-}
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- z-index:99;
- position:fixed;
- top: 0;
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- border:none;
- filter:alpha(opacity=0);
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- height:100%;
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- height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px');
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- clear:both;
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- margin-bottom:-1px;
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-/* @group Debugging Section */
-
-#debugging-toggle {
- text-align: center;
-}
-#debugging-toggle img {
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-
-#rdoc-debugging-section-dump {
- display: none;
- margin: 0 2em 2em;
- background: #ccc;
- border: 1px solid #999;
-}
-
-
-
-/* @end */
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: seq.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-03-19 16:29:08 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>amatch</li>
-
- <li>digest</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2007-2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
- <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
-
- <title>File: sff.rb [RDoc Documentation]</title>
-
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
-
- <script src="./js/jquery.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/thickbox-compressed.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/quicksearch.js" type="text/javascript"
- charset="utf-8"></script>
- <script src="./js/darkfish.js" type="text/javascript"
- charset="utf-8"></script>
-</head>
-
-<body class="file file-popup">
- <div id="metadata">
- <dl>
- <dt class="modified-date">Last Modified</dt>
- <dd class="modified-date">2011-02-11 19:55:38 +0100</dd>
-
-
- <dt class="requires">Requires</dt>
- <dd class="requires">
- <ul>
-
- <li>base36</li>
-
- </ul>
- </dd>
-
-
-
- </dl>
- </div>
-
- <div id="documentation">
-
- <div class="description">
- <h2>Description</h2>
- <p>
-Copyright (C) 2011 Martin A. Hansen.
-</p>
-
- </div>
-
- </div>
-</body>
-</html>
-
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'seq'
-require 'filesys'
-
-# Error class for all exceptions to do with FASTA.
-class FastaError < StandardError; end
-
-class Fasta < Filesys
- # Method to get the next FASTA entry form an ios and return this
- # as a Seq object. If no entry is found or eof then nil is returned.
- def get_entry
- block = @io.gets($/ + '>')
- return nil if block.nil?
-
- block.chomp!($/ + '>')
-
- (seq_name, seq) = block.split($/, 2)
-
- raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
-
- entry = Seq.new
- entry.type = @type.nil? ? nil : @type.downcase
- entry.seq = seq.gsub(/\s/, '')
- entry.seq_name = seq_name.sub(/^>/, '').rstrip
-
- raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
- raise FastaError, "Bad FASTA format" if entry.seq.empty?
-
- entry
- end
-
- # TODO - this should be some custom to_s method instead.
- def puts(record)
- if record.has_key? :SEQ_NAME and record.has_key? :SEQ
- @io.print ">#{record[:SEQ_NAME]}\n"
- @io.print "#{record[:SEQ]}\n"
- end
- end
-end
-
-
-__END__
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'seq'
-require 'filesys'
-
-# Error class for all exceptions to do with FASTQ.
-class FastqError < StandardError; end
-
-class Fastq < Filesys
- # Method to get the next FASTQ entry form an ios and return this
- # as a Seq object. If no entry is found or eof then nil is returned.
- def get_entry
- begin
- seq_name = @io.gets.chomp!
- seq = @io.gets.chomp!
- qual_name = @io.gets.chomp!
- qual = @io.gets.chomp!
-
- entry = Seq.new
- entry.type = @type.nil? ? nil : @type.downcase
- entry.seq = seq
- entry.seq_name = seq_name[1 .. seq_name.length]
- entry.qual = qual
-
- entry
- rescue
- nil
- end
- end
-
- # TODO - this should be some custom to_s method instead.
- def puts(record)
- if record.has_key? :SEQ_NAME and record.has_key? :SEQ
- @io.print ">#{record[:SEQ_NAME]}\n"
- @io.print "#{record[:SEQ]}\n"
- end
- end
-end
-
-
-__END__
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'zlib'
-
-# Error class for all exceptions to do with Filesys.
-class FilesysError < StandardError; end
-
-class Filesys
- include Enumerable
-
- # Class method that returns a path to a unique temporary file.
- # If no directory is specified reverts to the systems tmp directory.
- def self.tmpfile(tmp_dir = ENV["TMPDIR"])
- time = Time.now.to_i
- user = ENV["USER"]
- pid = $$
- path = tmp_dir + [user, time + pid, pid].join("_") + ".tmp"
- path
- end
-
- # Class method allowing open to be used on (zipped) files.
- # See File.open.
- def self.open(*args)
- args = *args
- file = args.first
-
- if file == "-"
- ios = self.new(STDIN)
- elsif File.pipe? file
- ios = self.new(File.open(*args))
- else
- ios = self.zopen(*args)
- end
-
- if block_given?
- begin
- yield ios
- ensure
- ios.close
- end
- else
- return ios
- end
- end
-
- def initialize(io, type=nil)
- @io = io
- @type = type
- end
-
- # Method to close ios.
- def close
- @io.close
- end
-
- # Iterator method for parsing entries.
- def each
- while entry = get_entry do
- yield entry
- end
- end
-
- private
-
- # Helper method to return an ios to a file that may be zipped in which case
- # the ios is unzipped on the fly. See File.open.
- def self.zopen(*args)
- ios = File.open(*args)
-
- begin
- ios = Zlib::GzipReader.new(ios)
- rescue
- ios.rewind
- end
-
- self.new(ios)
- end
-end
+++ /dev/null
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'seq'
-require 'filesys'
-
-# Error class for all exceptions to do with Genbank.
-class GenbankError < StandardError; end
-
-class Genbank < Filesys
- def initialize(io)
- @io = io
- @entry = []
- end
-
- # Iterator method for parsing Genbank entries.
- def each(hash_keys = nil, hash_feats = nil, hash_quals = nil)
- while @entry = get_entry do
- keys = get_keys(hash_keys)
- seq = get_seq
-
- features = GenbankFeatures.new(@entry, hash_feats, hash_quals)
-
- features.each do |record|
- keys.each_pair { |key,val| record[key] = val }
-
- loc = Locator.new(record[:LOCATOR], seq)
- record[:SEQ] = loc.subseq.seq
- record[:SEQ_LEN] = loc.subseq.length
- record[:STRAND] = loc.strand
- record[:S_BEG] = loc.s_beg
- record[:S_END] = loc.s_end
-
- yield record
- end
- end
- end
-
- private
-
- # Method to get the next Genbank entry form an ios and return this.
- def get_entry
- block = @io.gets("//" + $/)
- return nil if block.nil?
-
- block.chomp!("//" + $/ )
-
- entry = block.split $/
-
- return nil if entry.empty?
-
- entry
- end
-
- # Method to get the DNA sequence from a Genbank entry and return
- # this as a Seq object.
- def get_seq
- i = @entry.size
- j = i - 1
-
- while @entry[j] and @entry[j] !~ /^[A-Z]/
- j -= 1
- end
-
- seq = @entry[j + 1 .. i].join.delete(" 0123456789")
-
- Seq.new(nil, seq, "dna") if seq
- end
-
- # Method to get the base keys from Genbank entry and return these
- # in a hash.
- def get_keys(hash_keys)
- keys = {}
- i = 0
- j = 0
-
- while @entry[i] and @entry[i] !~ /^FEATURES/
- if @entry[i] =~ /^\s{0,3}([A-Z]{2})/
- if want_key?(hash_keys, $1)
- j = i + 1
-
- key, val = @entry[i].lstrip.split(/\s+/, 2)
-
- while @entry[j] and @entry[j] !~ /^\s{0,3}[A-Z]/
- val << @entry[j].lstrip
- j += 1
- end
-
- if keys[key.to_sym]
- keys[key.to_sym] << ";" + val
- else
- keys[key.to_sym] = val
- end
- end
- end
-
- j > i ? i = j : i += 1
- end
-
- keys
- end
-
- def want_key?(hash_keys, key)
- if hash_keys
- if hash_keys[key.to_sym]
- return true
- else
- return false
- end
- else
- return true
- end
- end
-end
-
-class GenbankFeatures
- @@i = 0
- @@j = 0
-
- def initialize(entry, hash_feats, hash_quals)
- @entry = entry
- @hash_feats = hash_feats
- @hash_quals = hash_quals
- end
-
- def each
- while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
- if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
- if want_feat? $1
- record = {}
-
- feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
-
- @@j = @@i + 1
-
- while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
- loc << @entry[@@j].lstrip
- @@j += 1
- end
-
- get_quals.each_pair { |k,v|
- record[k.upcase.to_sym] = v
- }
-
- record[:FEATURE] = feat
- record[:LOCATOR] = loc
-
- yield record
- end
- end
-
- @@j > @@i ? @@i = @@j : @@i += 1
- end
- end
-
- private
-
- def get_quals
- quals = {}
- k = 0
-
- while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
- if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
- qual = $1
- val = $2
-
- if want_qual? qual
- k = @@j + 1
-
- while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
- val << @entry[k].lstrip.chomp('"')
- k += 1
- end
-
- if quals[qual]
- quals[qual] << ";" + val
- else
- quals[qual] = val
- end
- end
- end
-
- k > @@j ? @@j = k : @@j += 1
- end
-
- quals
- end
-
- def want_feat?(feat)
- if @hash_feats
- if @hash_feats[feat.upcase.to_sym]
- return true
- else
- return false
- end
- else
- return true
- end
- end
-
- def want_qual?(qual)
- if @hash_quals
- if @hash_quals[qual.upcase.to_sym]
- return true
- else
- return false
- end
- else
- return true
- end
- end
-end
-
-
-# Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table locators.
-class LocatorError < StandardError; end
-
-class Locator
- attr_accessor :locator, :seq, :subseq
-
- def initialize(locator, seq)
- @locator = locator
- @seq = seq
- @subseq = Seq.new(nil, "", "dna")
- parse_locator(locator)
- end
-
- def strand
- if @locator.match("complement")
- return "-"
- else
- return "+"
- end
- end
-
- def s_beg
- if @locator =~ /(\d+)/
- return $1.to_i - 1
- end
- end
-
- def s_end
- if @locator.reverse =~ /(\d+)/
- return $1.reverse.to_i - 1
- end
- end
-
- private
-
- # Method that uses recursion to parse a locator string from a feature
- # table and fetches the appropriate subsequence. the operators
- # join(), complement(), and order() are handled.
- # the locator string is broken into a comma separated lists, and
- # modified if the parens donnot balance. otherwise the comma separated
- # list of ranges are stripped from operators, and the subsequence are
- # fetched and handled according to the operators.
- # SNP locators are also dealt with (single positions).
- def parse_locator(locator, join = nil, comp = nil, order = nil)
- intervals = locator.split(",")
-
- unless balance_parens?(intervals.first) # locator includes a join/comp/order of several ranges
- case locator
- when /^join\((.*)\)$/
- locator = $1
- join = true
- when /^complement\((.*)\)$/
- locator = $1
- comp = true
- when /^order\((.*)\)$/
- locator = $1
- order = true
- end
-
- parse_locator(locator, join, comp, order)
- else
- intervals.each do |interval|
- case interval
- when /^join\((.*)\)$/
- locator = $1
- join = true
- parse_locator(locator, join, comp, order)
- when /^complement\((.*)\)$/
- locator = $1
- comp = true
- parse_locator(locator, join, comp, order)
- when /^order\((.*)\)$/
- locator = $1
- order = true
- parse_locator(locator, join, comp, order)
- when /^[<>]?(\d+)[^\d]+(\d+)$/
- int_beg = $1.to_i - 1
- int_end = $2.to_i - 1
-
- newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
-
- unless newseq.seq.nil?
- newseq.revcomp if comp
-
- @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
- end
- when /^(\d+)$/
- pos = $1.to_i - 1
-
- newseq = Seq.new(nil, @seq.seq[pos], "dna")
-
- unless newseq.seq.nil?
- newseq.revcomp if comp
-
- @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
- end
- else
- $stderr.puts "WARNING: Could not match locator -> #{locator}";
- @subseq.seq << ""
- end
- end
- end
-
- return @subseq
- end
-
- def balance_parens?(locator)
- parens = 0
-
- locator.each_char do |char|
- case char
- when '(' then parens += 1
- when ')' then parens -= 1
- end
- end
-
- if parens == 0
- return true
- else
- return false
- end
- end
-end
-
-
-__END__
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'filesys'
-require 'open3'
-
-# Module containing code to locate nucleotide patterns in sequences allowing for
-# ambiguity codes and a given maximum mismatches, insertions, and deletions. The
-# pattern match engine is based on scan_for_matches.
-module Patscan
- # ------------------------------------------------------------------------------
- # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]])
- # -> Array
- # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]]) { |match|
- # block
- # }
- # -> Match
- #
- # ------------------------------------------------------------------------------
- # Method to iterate through a sequence to locate pattern matches starting
- # allowing for a maximum number of mismatches, insertions, and deletions.
- # Matches found in block context return the Match object. Otherwise matches are
- # returned in an Array.
- def scan(pattern, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
- @pattern = pattern + "[#{max_mismatches},#{max_insertions},#{max_deletions}]"
- matches = []
-
- pattern_file = Filesys.tmpfile
-
- File.open(pattern_file, mode = 'w') do |ios|
- ios.puts @pattern
- end
-
- cmd = "scan_for_matches #{pattern_file}"
-
- Open3.popen3(cmd) do |stdin, stdout, stderr|
- #raise SeqError, "scan_for_matches failed: #{stderr.gets}" unless stderr.empty?
-
- stdin << ">dummy\n#{self.seq}\n"
-
- stdin.close
-
- while block = stdout.gets($/ + ">")
- if block =~ />dummy:\[(\d+),(\d+)\]\n(.+)/
- start = $1.to_i
- stop = $2.to_i
- match = $3.delete(" ")
- length = stop - start
-
- if block_given?
- yield Match.new(start, length, match)
- else
- matches << Match.new(start, length, match)
- end
- end
- end
- end
-
- matches unless block_given?
- end
-
- class Match
- attr_reader :pos, :length, :match
-
- def initialize(pos, length, match)
- @pos = pos
- @length = length
- @match = match
- end
- end
-end
-
-__END__
-
-
-# Eeeeiiiii - this one is slower than scan_for_matches!
-
-
-# Module containing code to locate nucleotide patterns in sequences allowing for
-# ambiguity codes and a given maximum edit distance. Pattern match engine is based
-# on nrgrep.
-module Patscan
- # ------------------------------------------------------------------------------
- # str.scan(pattern[, max_edit_distance])
- # -> Array
- # str.scan(pattern[, max_edit_distance]) { |match|
- # block
- # }
- # -> Match
- #
- # ------------------------------------------------------------------------------
- # Method to iterate through a sequence to locate pattern matches starting
- # from a given position and allowing for a maximum edit distance.
- # Matches found in block context return the Match object. Otherwise matches are
- # returned in an Array.
- def scan(pattern, edit_distance = 0)
- @pattern = pattern.upcase
- matches = []
-
- pattern_disambiguate
-
- cmd = "nrgrep_coords"
- cmd << " -i"
- cmd << " -k #{edit_distance}s" if edit_distance > 0
- cmd << " #{@pattern}"
-
- Open3.popen3(cmd) do |stdin, stdout, stderr|
- stdin << self.seq
-
- stdin.close
-
- stdout.each_line do |line|
- if line =~ /\[(\d+), (\d+)\]: (.+)/
- start = $1.to_i
- stop = $2.to_i
- match = $3
- length = stop - start
-
- if block_given?
- yield Match.new(start, length, match)
- else
- matches << Match.new(start, length, match)
- end
- end
- end
- end
-
- matches unless block_given?
- end
-
- private
-
- def pattern_disambiguate
- case self.type
- when 'protein'
- @pattern.gsub!('J', '[IFVLWMAGCY]')
- @pattern.gsub!('O', '[TSHEDQNKR]')
- @pattern.gsub!('B', '[DN]')
- @pattern.gsub!('Z', '[EQ]')
- @pattern.gsub!('X', '.')
- when 'dna'
- @pattern.gsub!('R', '[AG]')
- @pattern.gsub!('Y', '[CT]')
- @pattern.gsub!('S', '[GC]')
- @pattern.gsub!('W', '[AT]')
- @pattern.gsub!('M', '[AC]')
- @pattern.gsub!('K', '[GT]')
- @pattern.gsub!('V', '[ACG]')
- @pattern.gsub!('H', '[ACT]')
- @pattern.gsub!('D', '[AGT]')
- @pattern.gsub!('B', '[CGT]')
- @pattern.gsub!('N', '.')
- when 'rna'
- else
- raise SeqError "unknown sequence type: #{self.type}"
- end
- end
-
- class Match
- attr_reader :pos, :length, :match
-
- def initialize(pos, length, match)
- @pos = pos
- @length = length
- @match = match
- end
- end
-end
-
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# IUPAC nucleotide pair ambiguity equivalents are saved in an
-# array of bit fields.
-
-BIT_A = 1 << 0
-BIT_T = 1 << 1
-BIT_C = 1 << 2
-BIT_G = 1 << 3
-
-EQUAL = Array.new(256, 0)
-EQUAL['A'.ord] = BIT_A
-EQUAL['a'.ord] = BIT_A
-EQUAL['T'.ord] = BIT_T
-EQUAL['t'.ord] = BIT_T
-EQUAL['U'.ord] = BIT_T
-EQUAL['u'.ord] = BIT_T
-EQUAL['C'.ord] = BIT_C
-EQUAL['c'.ord] = BIT_C
-EQUAL['G'.ord] = BIT_G
-EQUAL['g'.ord] = BIT_G
-EQUAL['M'.ord] = (BIT_A|BIT_C)
-EQUAL['m'.ord] = (BIT_A|BIT_C)
-EQUAL['R'.ord] = (BIT_A|BIT_G)
-EQUAL['r'.ord] = (BIT_A|BIT_G)
-EQUAL['W'.ord] = (BIT_A|BIT_T)
-EQUAL['w'.ord] = (BIT_A|BIT_T)
-EQUAL['S'.ord] = (BIT_C|BIT_G)
-EQUAL['s'.ord] = (BIT_C|BIT_G)
-EQUAL['Y'.ord] = (BIT_C|BIT_T)
-EQUAL['y'.ord] = (BIT_C|BIT_T)
-EQUAL['K'.ord] = (BIT_G|BIT_T)
-EQUAL['k'.ord] = (BIT_G|BIT_T)
-EQUAL['B'.ord] = (BIT_C|BIT_G|BIT_T)
-EQUAL['b'.ord] = (BIT_C|BIT_G|BIT_T)
-EQUAL['D'.ord] = (BIT_A|BIT_G|BIT_T)
-EQUAL['d'.ord] = (BIT_A|BIT_G|BIT_T)
-EQUAL['H'.ord] = (BIT_A|BIT_C|BIT_T)
-EQUAL['h'.ord] = (BIT_A|BIT_C|BIT_T)
-EQUAL['V'.ord] = (BIT_A|BIT_C|BIT_G)
-EQUAL['v'.ord] = (BIT_A|BIT_C|BIT_G)
-EQUAL['N'.ord] = (BIT_A|BIT_C|BIT_G|BIT_T)
-EQUAL['n'.ord] = (BIT_A|BIT_C|BIT_G|BIT_T)
-
-# Module containing code to locate nucleotide patterns in sequences allowing for
-# ambiguity codes and a given maximum edit distance.
-# Insertions are nucleotides found in the pattern but not in the sequence.
-# Deletions are nucleotides found in the sequence but not in the pattern.
-#
-# Inspired by the paper by Bruno Woltzenlogel Paleo (page 197):
-# http://www.logic.at/people/bruno/Papers/2007-GATE-ESSLLI.pdf
-module PatternMatcher
- # ------------------------------------------------------------------------------
- # str.match(pattern[, pos[, max_edit_distance]])
- # -> Match or nil
- #
- # ------------------------------------------------------------------------------
- # Method to locate the next pattern match starting from a given position. A match
- # is allowed to contain a given maximum edit distance. If a match is located a
- # Match object will be returned otherwise nil.
- def match(pattern, pos = 0, max_edit_distance = 0)
- @pattern = pattern
- @pos = pos
- @max_edit_distance = max_edit_distance
- @vector = vector_init
-
- while @pos < @seq.length
- vector_update
-
- return match_new if match_found?
-
- @pos += 1
- end
- end
-
- # ------------------------------------------------------------------------------
- # str.scan(pattern[, pos[, max_edit_distance]])
- # -> Array
- # str.scan(pattern[, pos[, max_edit_distance]]) { |match|
- # block
- # }
- # -> Match
- #
- # ------------------------------------------------------------------------------
- # Method to iterate through a sequence to locate pattern matches starting
- # from a given position and allowing for a maximum edit distance.
- # Matches found in block context return the Match object. Otherwise matches are
- # returned in an Array.
- def scan(pattern, pos = 0, max_edit_distance = 0)
- matches = []
-
- while match = match(pattern, pos, max_edit_distance)
- if block_given?
- yield match
- else
- matches << match
- end
-
- pos = match.pos + 1
- end
-
- return matches unless block_given?
- end
-
- private
-
- # Method to initailize the score vector and return this.
- def vector_init
- vector = []
-
- (0 ... @pattern.length + 1).each do |i|
- vector[i] = Score.new(matches = 0, mismatches = 0, insertions = i)
- end
-
- vector
- end
-
- # Method to update the score vector.
- def vector_update
- score_diag = @vector[0]
- score_up = Score.new # insertion
- score_left = @vector[1] # deletion
-
- (0 ... @pattern.length).each do |i|
- if match?(@seq[@pos], @pattern[i])
- new_score = score_diag.dup
- new_score.matches += 1
- else
- if deletion?(score_diag, score_up, score_left)
- new_score = score_left.dup
- new_score.deletions += 1
- elsif mismatch?(score_diag, score_up, score_left)
- new_score = score_diag.dup
- new_score.mismatches += 1
- elsif insertion?(score_diag, score_up, score_left)
- new_score = score_up.dup
- new_score.insertions += 1
- end
- end
-
- score_diag = @vector[i + 1]
- score_up = new_score
- score_left = @vector[i + 2]
-
- @vector[i + 1] = new_score
- end
- end
-
- # Method to determine if a match occurred.
- def match?(char1, char2)
- (EQUAL[char1.ord] & EQUAL[char2.ord]) != 0
- end
-
- # Method to determine if a mismatch occured.
- def mismatch?(score_diag, score_up, score_left)
- if score_diag.edit_distance <= score_up.edit_distance and
- score_diag.edit_distance <= score_left.edit_distance
- true
- end
- end
-
- # Method to determine if an insertion occured.
- def insertion?(score_diag, score_up, score_left)
- if score_up.edit_distance <= score_diag.edit_distance and
- score_up.edit_distance <= score_left.edit_distance
- true
- end
- end
-
- # Method to determine if a deletion occured.
- def deletion?(score_diag, score_up, score_left)
- if score_left.edit_distance <= score_diag.edit_distance and
- score_left.edit_distance <= score_up.edit_distance
- true
- end
- end
-
- # Method to print the score vector.
- def vector_print
- @vector.each do |s|
- puts s
- end
-
- puts
- end
-
- # Method that returns a Match object initialized with
- # information from the score vector.
- def match_new
- matches = @vector.last.matches
- mismatches = @vector.last.mismatches
- insertions = @vector.last.insertions
- deletions = @vector.last.deletions
- length = @pattern.length - insertions + deletions
- pos = @pos - length + 1
- match = @seq[pos ... pos + length]
-
- Match.new(pos, match, matches, mismatches, insertions, deletions, length)
- end
-
- # Method that determines if a match was found by analyzing the score vector.
- def match_found?
- if @vector.last.edit_distance <= @max_edit_distance
- true
- end
- end
-
- # Class to instantiate Score objects that holds score information.
- class Score
- attr_accessor :matches, :mismatches, :insertions, :deletions
-
- def initialize(matches = 0, mismatches = 0, insertions = 0, deletions = 0)
- @matches = matches
- @mismatches = mismatches
- @insertions = insertions
- @deletions = deletions
- end
-
- # Method to calculate and return the edit distance.
- def edit_distance
- self.mismatches + self.insertions + self.deletions
- end
-
- private
-
- def to_s
- "(#{[self.matches, self.mismatches, self.insertions, self.deletions].join(',')})"
- end
- end
-
- # Class for creating Match objects which contain the description of a
- # match between a nucleotide sequence and a pattern.
- class Match
- attr_reader :pos, :match, :matches, :mismatches, :insertions, :deletions, :edit_distance, :length
-
- def initialize(pos, match, matches, mismatches, insertions, deletions, length)
- @pos = pos
- @match = match
- @matches = matches
- @mismatches = mismatches
- @insertions = insertions
- @deletions = deletions
- @edit_distance = mismatches + insertions + deletions
- @length = length
- end
- end
-end
+++ /dev/null
-# Copyright (C) 2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'genbank'
-
-# Class for running the Prodigal gene finder.
-# http://prodigal.ornl.gov/
-class Prodigal
- include Enumerable
-
- # Method to initialize a Prodigal object
- # given a temporary infile, outfile and options hash.
- def initialize(infile, outfile, options)
- @infile = infile
- @outfile = outfile
- @options = options
- end
-
- # Method to run Prodigal.
- def run
- commands = []
- commands << "prodigal"
- commands << "-c" if @options[:full]
- commands << "-p #{@options[:procedure]}"
- commands << "-i #{@infile}"
- commands << "-o #{@outfile}"
-
- execute(commands, @options[:verbose])
- end
-
- # Method for iterating over the Prodigal results,
- # which are in GenBank format.
- def each
- Genbank.open(@outfile, mode='r') do |gb|
- gb.each do |entry|
- yield entry
- end
- end
- end
-
- # Method that returns the sum of the predicted gene lengths.
- def coverage
- coverage = 0
-
- self.each do |gb|
- coverage += gb[:S_END] - gb[:S_BEG]
- end
-
- coverage
- end
-
- private
-
- # Method to execute commands on the command line.
- # TODO this wants to be in a module on its own.
- def execute(commands, verbose = false)
- commands.unshift "nice -n 19"
- commands.push "> /dev/null 2>&1" unless verbose
-
- command = commands.join(" ")
-
- begin
- system(command)
- raise "Command failed: #{command}" unless $?.success?
- rescue
- $stderr.puts "Command failed: #{command}"
- end
- end
-end
-
-
-__END__
+++ /dev/null
-# Copyright (C) 2007-2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'digest'
-#require 'patscan'
-require 'patternmatcher'
-
-# Residue alphabets
-DNA = %w[a t c g]
-RNA = %w[a u c g]
-PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
-INDELS = %w[. - _ ~]
-
-# Quality scores bases
-SCORE_PHRED = 33
-SCORE_ILLUMINA = 64
-
-# Error class for all exceptions to do with Seq.
-class SeqError < StandardError; end
-
-class Seq
- #include Patscan
- include PatternMatcher
-
- attr_accessor :seq_name, :seq, :type, :qual
-
- # Method that generates all possible oligos of a specifed length and type.
- def self.generate_oligos(length, type)
- raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
-
- case type.downcase
- when /dna/ then alph = DNA
- when /rna/ then alph = RNA
- when /protein/ then alph = PROTEIN
- else
- raise SeqError, "Unknown sequence type: #{type}"
- end
-
- oligos = [""]
-
- (1 .. length).each do
- list = []
-
- oligos.each do |oligo|
- alph.each do |char|
- list << oligo + char
- end
- end
-
- oligos = list
- end
-
- oligos
- end
-
- # Initialize a sequence object with the following arguments:
- # - seq_name: Name of the sequence.
- # - seq: The sequence.
- # - type: The sequence type - DNA, RNA, or protein
- # - qual: An Illumina type quality scores string.
- def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
- @seq_name = seq_name
- @seq = seq
- @type = type
- @qual = qual
- end
-
- # Returns the length of a sequence.
- def length
- self.seq.nil? ? 0 : self.seq.length
- end
-
- alias :len :length
-
- # Return the number indels in a sequence.
- def indels
- regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
- self.seq.scan(regex).size
- end
-
- # Method that returns true is a given sequence type is DNA.
- def is_dna?
- self.type == 'dna'
- end
-
- # Method that returns true is a given sequence type is RNA.
- def is_rna?
- self.type == 'rna'
- end
-
- # Method that returns true is a given sequence type is protein.
- def is_protein?
- self.type == 'protein'
- end
-
- # Method to transcribe DNA to RNA.
- def to_rna
- raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
- raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
- self.type = 'rna'
- self.seq.tr!('Tt','Uu')
- end
-
- # Method to reverse-transcribe RNA to DNA.
- def to_dna
- raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
- raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
-
- self.type = 'dna'
- self.seq.tr!('Uu','Tt')
- end
-
- # Method that given a Seq entry returns a Biopieces record (a hash).
- def to_bp
- raise SeqError, "Missing seq_name" if self.seq_name.nil?
- raise SeqError, "Missing seq" if self.seq.nil?
-
- record = {}
- record[:SEQ_NAME] = self.seq_name
- record[:SEQ] = self.seq
- record[:SEQ_LEN] = self.length
- record[:SCORES] = self.qual if self.qual
- record
- end
-
- # Method that given a Seq entry returns a FASTA entry (a string).
- def to_fasta(wrap = nil)
- raise SeqError, "Missing seq_name" if self.seq_name.nil?
- raise SeqError, "Missing seq" if self.seq.nil?
-
- seq_name = self.seq_name
- seq = self.seq
-
- unless wrap.nil?
- seq.gsub!(/(.{#{wrap}})/) do |match|
- match << "\n"
- end
-
- seq.chomp!
- end
-
- ">#{seq_name}\n#{seq}\n"
- end
-
- # Method that generates a unique key for a
- # DNA sequence and return this key as a Fixnum.
- def to_key
- key = 0
-
- self.seq.upcase.each_char do |char|
- key <<= 2
-
- case char
- when 'A' then key |= 0
- when 'C' then key |= 1
- when 'G' then key |= 2
- when 'T' then key |= 3
- else raise SeqError, "Bad residue: #{char}"
- end
- end
-
- key
- end
-
- # Method to reverse complement sequence.
- def reverse_complement
- self.reverse
- self.complement
- end
-
- alias :revcomp :reverse_complement
-
- # Method to reverse the sequence.
- def reverse
- self.seq.reverse!
- end
-
- # Method that complements sequence including ambiguity codes.
- def complement
- raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
-
- if self.is_dna?
- self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
- elsif self.is_rna?
- self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
- else
- raise SeqError, "Cannot complement sequence type: #{self.type}"
- end
- end
-
- # Method that generates a random sequence of a given length and type.
- def generate(length, type)
- raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
-
- case type.downcase
- when "dna"
- alph = DNA
- when "rna"
- alph = RNA
- when "protein"
- alph = PROTEIN
- else
- raise SeqError, "Unknown sequence type: #{type}"
- end
-
- seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
- self.seq = seq_new
- self.type = type.downcase
- seq_new
- end
-
- # Method that returns a subsequence of from a given start position
- # and of a given length.
- def subseq(start, length = self.length - start)
- raise SeqError, "subsequence start: #{start} < 0" if start < 0
- raise SeqError, "subsequence length: #{length} < 1" if length <= 0
- raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
- stop = start + length - 1
-
- seq = self.seq[start .. stop]
- qual = self.qual[start .. stop] unless self.qual.nil?
-
- Seq.new(self.seq_name, seq, self.type, qual)
- end
-
- # Method that replaces a sequence with a subsequence from a given start position
- # and of a given length.
- def subseq!(start, length = self.length - start)
- raise SeqError, "subsequence start: #{start} < 0" if start < 0
- raise SeqError, "subsequence length: #{length} < 1" if length <= 0
- raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
- stop = start + length - 1
-
- self.seq = self.seq[start .. stop]
- self.qual = self.qual[start .. stop] unless self.qual.nil?
- end
-
- # Method that returns a subsequence of a given length
- # beginning at a random position.
- def subseq_rand(length)
- if self.length - length + 1 == 0
- start = 0
- else
- start = rand(self.length - length + 1)
- end
-
- self.subseq(start, length)
- end
-
- # Method that returns the residue compositions of a sequence in
- # a hash where the key is the residue and the value is the residue
- # count.
- def composition
- comp = Hash.new(0);
-
- self.seq.upcase.each_char do |char|
- comp[char] += 1
- end
-
- comp
- end
-
- # Method that returns the length of the longest homopolymeric stretch
- # found in a sequence.
- def homopol_max(min = 1)
- return 0 if self.seq.nil? or self.seq.empty?
-
- found = false
-
- self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
- found = true
- min = match.size > min ? match.size : min
- end
-
- return 0 unless found
-
- min
- end
-
- # Method that returns the percentage of hard masked residues
- # or N's in a sequence.
- def hard_mask
- ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
- end
-
- # Method that returns the percentage of soft masked residues
- # or lower cased residues in a sequence.
- def soft_mask
- ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
- end
-
- # Method to convert the quality scores from a specified base
- # to another base.
- def convert_phred2illumina!
- self.qual.gsub!(/./) do |score|
- score_phred = score.ord - SCORE_PHRED
- raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
- score_illumina = score_phred + SCORE_ILLUMINA
- score = score_illumina.chr
- end
- end
-
- # Method to convert the quality scores from Solexa odd/ratio to
- # Illumina format.
- def convert_solexa2illumina!
- self.qual.gsub!(/./) do |score|
- score = solexa_char2illumina_char(score)
- end
- end
-
- private
-
- # Method to convert a Solexa score (odd ratio) to
- # a phred (probability) integer score.
- def solexa2phred(score)
- (10.0 * Math.log(10.0 ** (score / 10.0) + 1.0, 10)).to_i
- end
-
- # Method to convert a Solexa score encoded using base
- # 64 ASCII to a Phred score encoded using base 64 ASCII.
- def solexa_char2illumina_char(char)
- score_solexa = char.ord - 64
- score_phred = solexa2phred(score_solexa)
- (score_phred + 64).chr
- end
-end
-
-__END__
+++ /dev/null
-# Copyright (C) 2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'base36'
-
-# Error class for all exceptions to do with SFF.
-class SFFError < StandardError; end
-
-BIT_SHIFT = 12
-BIT_MASK = (1 << BIT_SHIFT) - 1
-
-# Class containing methods to parse SFF files:
-# http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff
-class SFF
- include Enumerable
-
- @@count = 0
-
- # Class method for opening SFF files.
- def self.open(*args)
- ios = File.open(*args)
-
- if block_given?
- begin
- yield self.new(ios)
- ensure
- ios.close
- end
- else
- return self.new(ios)
- end
- end
-
- # Method to initialize an SFF object along with
- # instance variables pertaining to the SFF header
- # section.
- def initialize(io)
- @io = io
- @magic_number = 0
- @version = ""
- @index_offset = 0
- @index_length = 0
- @number_of_reads = 0
- @header_length = 0
- @key_length = 0
- @number_of_flows_per_read = 0
- @flowgram_format_code = 0
- @flow_chars = ""
- @key_sequence = ""
- @eight_byte_padding = 0
-
- header_parse
- end
-
- # Method to close ios.
- def close
- @io.close
- end
-
- # Method to iterate over each SFF entry.
- def each
- while (read = read_parse) do
- yield read
- end
-
- self # conventionally
- end
-
- private
-
- # Method to parse the SFF file's header section
- # and load the information into the instance variables.
- def header_parse
- template = "NC4N2NNnnnC"
- bits_in_uint = 32
-
- data = @io.read(31).unpack(template)
-
- @magic_number = data[0]
- @version = data[1 .. 4].join ""
- @index_offset = (data[5] << bits_in_uint) | data[6]
- @index_length = data[7]
- @number_of_reads = data[8]
- @header_length = data[9]
- @key_length = data[10]
- @number_of_flows_per_read = data[11]
- @flowgram_format_code = data[12]
- @flow_chars = @io.read(@number_of_flows_per_read).unpack("A*").join ""
- @key_sequence = @io.read(@key_length).unpack("A*").join ""
-
- fast_forward
-
- check_magic_number
- check_version
- check_header_length
- end
-
- # Method that reads the eight_byte_padding field found at the end of the
- # data section and fast forwards, i.e. move the file read pointer,
- # so that the length of the section is divisible by 8.
- def fast_forward
- eight_byte_padding = 8 - (@io.pos % 8)
-
- @io.read(eight_byte_padding) unless eight_byte_padding == 8
- end
-
- # Method to parse a read section of an SFF file.
- def read_parse
- return nil if @number_of_reads == @@count
-
- template = "nnNnnnn"
-
- read = Read.new()
-
- data = @io.read(16).unpack(template)
-
- read.read_header_length = data[0]
- read.name_length = data[1]
- read.number_of_bases = data[2]
- read.clip_qual_left = data[3]
- read.clip_qual_right = data[4]
- read.clip_adapter_left = data[5]
- read.clip_adaptor_right = data[6]
- read.name = @io.read(read.name_length).unpack("A*").join ""
-
- fast_forward
-
- @io.read(2 * @number_of_flows_per_read) # skip through flowgram_values
- @io.read(read.number_of_bases) # skip through flow_index_per_base
-
- # NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.
- # read.flowgram_values = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }
- # flow_index_per_base = @io.read(read.number_of_bases).unpack("C*")
- # (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }
- # read.flow_index_per_base = flow_index_per_base
-
- read.bases = @io.read(read.number_of_bases).unpack("A*").join ""
- read.quality_scores = @io.read(read.number_of_bases).unpack("C*")
-
- fast_forward
-
- @@count += 1
-
- read
- end
-
- # Method to check the magic number of an SFF file.
- # Raises an error if the magic number don't match.
- def check_magic_number
- raise SFFError, "Badly formatted SFF file." unless @magic_number == 779314790
- end
-
- # Method to check the version number of an SFF file.
- # Raises an error if the version don't match.
- def check_version
- raise SFFError, "Wrong version: #{@version}" unless @version.to_i == 1
- end
-
- # Method to check the header length of an SFF file.
- # Raises an error if the header length don't match
- # the file position after reading the header section.
- def check_header_length
- raise SFFError, "Bad header length: #{header_length}" unless @io.pos == @header_length
- end
-end
-
-# Class containing data accessor methods for an SFF entry and methods
-# for manipulating this entry.
-class Read
- attr_accessor :read_header_length, :name_length, :number_of_bases,
- :clip_qual_left, :clip_qual_right, :clip_adapter_left, :clip_adaptor_right,
- :name, :flowgram_values, :flow_index_per_base, :bases, :quality_scores,
- :x_pos, :y_pos
-
- # Method that converts a Read object's data to a Biopiece record (a hash).
- def to_bp
- coordinates_get
-
- hash = {}
-
- hash[:SEQ_NAME] = self.name
- hash[:SEQ] = self.bases
- hash[:SEQ_LEN] = self.bases.length
- hash[:CLIP_QUAL_LEFT] = self.clip_qual_left - 1
- hash[:CLIP_QUAL_RIGHT] = self.clip_qual_right - 1
- hash[:CLIP_ADAPTOR_LEFT] = self.clip_adapter_left - 1
- hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
- hash[:SCORES] = self.quality_scores.map { |i| (i += 64).chr }.join ""
- hash[:X_POS] = self.x_pos
- hash[:Y_POS] = self.y_pos
-
- hash
- end
-
- # Method that soft masks the sequence (i.e. lowercases sequence) according to
- # clip_qual_left and clip_qual_right information.
- def mask
- left = self.bases[0 ... self.clip_qual_left - 1].downcase
- middle = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
- right = self.bases[self.clip_qual_right ... self.bases.length].downcase
-
- self.bases = left + middle + right
- end
-
- # Method that clips sequence (i.e. trims) according to
- # clip_qual_left and clip_qual_right information.
- def clip
- self.bases = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
- self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
- end
-
- private
-
- # Method that extracts the X/Y coordinates from
- # an SFF read name encoded with base36.
- def coordinates_get
- base36 = self.name[-5, 5]
- num = Base36.decode(base36)
-
- self.x_pos = num >> BIT_SHIFT
- self.y_pos = num & BIT_MASK
- end
-end
-
-__END__
-
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2011 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'test/unit'
-require 'base36'
-require 'pp'
-
-class Base36Test < Test::Unit::TestCase
- def test_Base36_encode_with_non_fixnum_value_raises
- assert_raise(Base36Error) { Base36.encode("foo") }
- end
-
- def test_Base36_encode_returns_correctly
- assert_equal("AWVHI", Base36.encode(1053908))
- end
-
- def test_Base36_decode_with_empty_value_raises
- assert_raise(Base36Error) { Base36.decode("") }
- end
-
- def test_Base36_decode_returns_correctly
- assert_equal(1053908, Base36.decode("AWVHI"))
- end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'test/unit'
-require 'biopieces'
-require 'pp'
-
-TYPES = %w[flag string list int uint float file file! files files! dir dir! genome]
-DUMMY_FILE = __FILE__
-SCRIPT_PATH = "write_fasta"
-
-class BiopiecesTest < Test::Unit::TestCase
-
- def setup
- @input = StringIO.new
- @output = StringIO.new
- @bp = Biopieces.new(true, @input, @output)
- end
-
- # >>>>>>>>>>>>>>>>>>>> Testing Options.new <<<<<<<<<<<<<<<<<<<<
-
- def test_Biopieces_parse_with_all_cast_keys_dont_raise
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_illegal_long_cast_values_raises
- [nil, true, false, 1, 0, "a"].each do |long|
- argv = []
- casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_long_cast_values_dont_raise
- ["foo", "!!", "0123"].each do |long|
- argv = []
- casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_short_cast_values_raises
- [nil, true, false, "foo"].each do |short|
- argv = []
- casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_short_cast_values_dont_raise
- ["!", "1", "a"].each do |short|
- argv = []
- casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_type_cast_values_raises
- [nil, true, false, "foo", 12, 0].each do |type|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_type_cast_values_dont_raise
- TYPES.each do |type|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_mandatory_cast_values_raises
- ["yes", 12, 0, nil].each do |mandatory|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_mandatory_cast_values_dont_raise
- [true, false].each do |mandatory|
- argv = [ "--foo", "1" ]
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_default_cast_values_raises
- [true, false, [], {}].each do |default|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_default_cast_values_dont_raise
- [nil, 0, 1, -1].each do |default|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_allowed_cast_values_raises
- [true, false, {}, [], 0, 0.1].each do |allowed|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_allowed_cast_values_dont_raise
- ["foo,bar,0",nil].each do |allowed|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_illegal_disallowed_cast_values_raises
- [true, false, {}, [], 0, 0.1].each do |disallowed|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_legal_disallowed_cast_values_dont_raise
- ["foo,bar,0",nil].each do |disallowed|
- argv = []
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_duplicate_long_cast_values_raises
- argv = []
- casts = []
- casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- casts << {:long=>"foo", :short=>"b", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_duplicate_short_cast_values_raises
- argv = []
- casts = []
- casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- casts << {:long=>"bar", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_without_duplicate_long_and_short_cast_values_dont_raise
- argv = []
- casts = []
- casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- casts << {:long=>"bar", :short=>"b", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
- assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- # >>>>>>>>>>>>>>>>>>>> Testing Options.parse <<<<<<<<<<<<<<<<<<<<
-
- def test_Biopieces_parse_with_empty_argv_and_missing_wiki_file_raises
- argv = []
- casts = []
- assert_raise(RuntimeError) { @bp.parse(argv,casts, "foo") }
- end
-
- def test_Biopieces_parse_with_empty_argv_and_existing_wiki_file_dont_raise
- argv = []
- casts = []
- assert_nothing_raised { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_help_in_argv_and_existing_wiki_output_long_usage
- argv = ["--help"]
- assert_nothing_raised { @bp.parse(argv,[],SCRIPT_PATH) }
- end
-
-# # FIXME This one fails because any argument to a flag is ignored and the flag value is set to true. Should it raise?
-# test "Options.parse with type cast flag with an argument raises
-# casts = [{:long=>"foo", :short=>"f", :type=>"flag", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
-# opt_parser = Options.new(casts)
-# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "bar"],SCRIPT_PATH) }
-# end
-
- def test_Biopieces_parse_with_stream_in_argv_returns_correct_options
- argv = ["--stream_in", DUMMY_FILE]
- options = @bp.parse(argv,[],SCRIPT_PATH)
- assert_equal([DUMMY_FILE], options[:stream_in])
- end
-
- def test_Biopieces_parse_with_I_argv_returns_correct_options
- argv = ["-I", DUMMY_FILE]
- casts = []
- options = @bp.parse(argv, casts, SCRIPT_PATH)
- assert_equal([DUMMY_FILE], options[:stream_in])
- end
-
- def test_Biopieces_parse_use_cast_default_value_if_no_argument_given
- argv = ["-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
- options = @bp.parse(argv, casts, SCRIPT_PATH)
- assert_equal(options[:foo], "bar")
- end
-
- def test_Biopieces_parse_dont_use_default_value_if_argument_given
- argv = ["--foo", "bleh", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
- options = @bp.parse(argv, casts, SCRIPT_PATH)
- assert_equal(options[:foo], "bleh".to_sym)
- end
-
- def test_Biopieces_parse_with_mandatory_cast_and_no_argument_raises
- argv = ["-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_mandatory_cast_and_argument_dont_raise
- argv = ["--foo", "bar", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
- end
-
-# # This one results in an error: "OptionParser::InvalidArgument: invalid argument: --foo bar"
-# # So it appears that this is tested in OptionParser already.
-# test "Options.parse with type cast int and non-int value raises" do
-# ["bar" ].each do |val| # what about nil, false, true, [], {}, 0.1 ?
-# casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
-# opt_parser = Options.new(casts)
-# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "#{val}"],SCRIPT_PATH) }
-# end
-# end
-
- def test_Biopieces_parse_with_type_cast_int_dont_raise
- [0,-1,1,327649123746293746374276347824].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
- end
- end
-
- # TODO similar test for uint as "test "Options.parse with type cast int and non-int value raises" do"
-
- def test_Biopieces_parse_with_type_cast_uint_dont_raise
- [0,1,327649123746293746374276347824].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"uint", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_file_cast_and_file_dont_exists_raises
- argv = ["--foo", "bleh", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_file_cast_and_existing_file_dont_raise
- argv = ["--foo", DUMMY_FILE, "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_files_cast_and_a_file_dont_exists_raises
- argv = ["--foo", DUMMY_FILE + ",bleh", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_files_cast_and_files_exists_dont_raise
- argv = ["--foo", DUMMY_FILE + "," + DUMMY_FILE, "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- # TODO replace the absolute part below the file location with File.dirname(__FILE__)
- def test_Biopieces_parse_with_glob_argument_expands_correctly
- flunk("This test is weird")
- argv = ["--foo", "/Users/maasha/unit_test/foo*,/Users/maasha/unit_test/my_dir/*.fna", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- options = @bp.parse(argv, casts, SCRIPT_PATH)
- assert_equal(["/Users/maasha/unit_test/foo.fna", "/Users/maasha/unit_test/my_dir/bar.fna"], options[:foo])
- end
-
- def test_Biopieces_parse_with_dir_cast_and_dir_dont_exists_raises
- argv = ["--foo", "bleh", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_dir_cast_and_dir_exists_dont_raise
- argv = ["--foo", "/", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
-
- def test_Biopieces_parse_with_allowed_cast_and_not_allowed_value_raises
- ["bleh", "2", "3.3"].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
- assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_allowed_cast_and_allowed_values_dont_raise
- ["0", "-1", "0.0", "1", "bar"].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_disallowed_cast_and_disallowed_value_raises
- ["0", "-1", "0.0", "1", "bar"].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
- assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-
- def test_Biopieces_parse_with_disallowed_cast_and_allowed_values_dont_raise
- ["bleh", "2", "3.3"].each do |val|
- argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
- casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
- assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
- end
- end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-require 'bitarray'
-require 'test/unit'
-require 'pp'
-
-class TestBitArray < Test::Unit::TestCase
- def setup
- @ba = BitArray.new(10)
- end
-
- def test_BitArray_initialize_raises_on_bad_sizes
- [ -1, 0, 1.1, "a" ].each do |size|
- assert_raise(BitArrayError) { BitArray.new(size) }
- end
- end
-
- def test_BitArray_initialize_dont_raise_on_ok_sizes
- [ 1, 10, 1000 ].each do |size|
- assert_nothing_raised { BitArray.new(size) }
- end
- end
-
- def test_BitArray_size_returns_correctly
- assert_equal(10, @ba.size)
- end
-
- def test_BitArray_to_s_returns_correctly
- assert_equal("0000000000", @ba.to_s)
- end
-
- def test_BitArray_bit_set_with_bad_pos_raises
- [-1, 10, 1.1].each do |pos|
- assert_raise(BitArrayError) { @ba.bit_set(pos) }
- end
- end
-
- def test_BitArray_bit_set
- str = "0000000000"
-
- (0.upto 9).each do |pos|
- @ba.bit_set(pos)
- str[pos] = "1"
- assert_equal(str, @ba.to_s)
- end
- end
-
- def test_BitArray_bit_set_questionmark_with_bad_pos_raises
- [-1, 10, 1.1].each do |pos|
- assert_raise(BitArrayError) { @ba.bit_set?(pos) }
- end
- end
-
- def test_BitArray_bit_set_questionmark
- (0.upto 9).each do |pos|
- @ba.bit_set(pos)
- assert_equal(true, @ba.bit_set?(pos))
- end
- end
-
- def test_BitArray_bits_on_returns_correctly
- @ba.bit_set(4)
- @ba.bit_set(0)
- @ba.bit_set(1)
- assert_equal(3, @ba.bits_on)
- end
-
- def test_BitArray_bits_off_returns_correctly
- @ba.bit_set(4)
- assert_equal(9, @ba.bits_off)
- end
-
- def test_BitArray_AND_with_uneven_sizes_raises
- ba = BitArray.new(11)
- assert_raise(BitArrayError) { @ba & ba }
- end
-
- def test_BitArray_AND_returns_correctly
- ba = BitArray.new(10)
- @ba.bit_set(4)
- @ba.bit_set(5)
- ba.bit_set(5)
- ba.bit_set(6)
- assert_equal( "0000010000", (@ba & ba).to_s)
- end
-
- def test_BitArray_OR_with_uneven_sizes_raises
- ba = BitArray.new(11)
- assert_raise(BitArrayError) { @ba | ba }
- end
-
- def test_BitArray_OR_returns_correctly
- ba = BitArray.new(10)
- @ba.bit_set(4)
- @ba.bit_set(5)
- ba.bit_set(5)
- ba.bit_set(6)
- assert_equal( "0000111000", (@ba | ba).to_s)
- end
-
- def test_BitArray_XOR_with_uneven_sizes_raises
- ba = BitArray.new(11)
- assert_raise(BitArrayError) { @ba ^ ba }
- end
-
- def test_BitArray_XOR_returns_correctly
- ba = BitArray.new(10)
- @ba.bit_set(4)
- @ba.bit_set(5)
- ba.bit_set(5)
- ba.bit_set(6)
- assert_equal( "0000101000", (@ba ^ ba).to_s)
- end
-end
-
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-require 'bits'
-require 'test/unit'
-require 'pp'
-
-class TestBits < Test::Unit::TestCase
- def test_Bits_hamming_dist_with_uneven_lengths_raises
- assert_raises(StringError) { String.hamming_dist("ATCG", "ATC") }
- end
-
- def test_Bits_hamming_dist_with_even_lengths_dont_raise
- assert_nothing_raised { String.hamming_dist("ATCG", "ATCG") }
- end
-
- def test_Bits_hamming_dist_returns_correctly
- assert_equal(0, String.hamming_dist("ATCG", "ATCG"))
- assert_equal(1, String.hamming_dist("ATCX", "ATCG"))
- assert_equal(2, String.hamming_dist("ATXX", "ATCG"))
- assert_equal(2, String.hamming_dist("ATcg", "ATCG"))
- assert_equal(3, String.hamming_dist("AXXX", "ATCG"))
- assert_equal(4, String.hamming_dist("XXXX", "ATCG"))
- end
-
- def test_Bits_AND_with_equal_length_returns_correctly
- assert_equal("ABCD", "abcd" & "____")
- end
-
- def test_Bits_AND_with_unequal_length_returns_correctly
- assert_equal("JAPH\n", "japh\nJunk" & '_____')
- assert_equal("JAPH\n", '_____' & "japh\nJunk")
- end
-
- def test_Bits_OR_with_equal_length_returns_correctly
- assert_equal("abcd", "ab " | " cd")
- end
-
- def test_Bits_OR_with_unequal_length_returns_correctly
- assert_equal("japh\n", "JA" | " ph\n")
- assert_equal("japh\n", " ph\n" | "JA")
- end
-
- def test_Bits_XOR_with_equal_length_returns_correctly
- assert_equal("ABCD", "ab " ^ " cd")
- end
-
- def test_Bits_XOR_with_unequal_length_returns_correctly
- assert_equal("JAPH", "j p \n" ^ " a h")
- assert_equal("JAPH", " a h" ^ "j p \n")
- end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-
-require 'seq'
-require 'test/unit'
-require 'pp'
-
-class TestDigest < Test::Unit::TestCase
- def setup
- @entry = Seq.new
- end
-
- def test_Digest_new_raises_on_bad_pattern_residue
- assert_raise(DigestError) { Digest.new(@entry, "X", 4) }
- end
-
- def test_Digest_new_dont_raise_on_ok_pattern_residue
- assert_nothing_raised { Digest.new(@entry, "AGCUTRYWSMKHDVBNagcutrywsmkhdvbn", 4) }
- end
-
- def test_Digest_each
- @entry.seq = "aaaaTTTTbbbbTTTT"
- digest = Digest.new(@entry, "TTNT", 1)
- assert_equal("aaaaT", digest.first.seq)
- end
-end
-
-
-__END__
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'test/unit'
-require 'fasta'
-require 'stringio'
-require 'pp'
-
-class FastaTest < Test::Unit::TestCase
- def test_Fasta_get_entry_obtains_the_correct_seq_name
- fasta = Fasta.new(StringIO.new(">test\nATCG\n"))
- assert_equal(fasta.get_entry.seq_name, "test")
- end
-
- def test_Fasta_get_entry_obtains_the_correct_seq_without_trailing_newlines
- fasta = Fasta.new(StringIO.new(">test\nATCG"))
- assert_equal(fasta.get_entry.seq, "ATCG")
- end
-
- def test_Fasta_get_entry_obtains_the_correct_seq_with_trailing_newlines
- fasta = Fasta.new(StringIO.new(">test\nATCG\n\n\n"))
- assert_equal(fasta.get_entry.seq, "ATCG")
- end
-
- def test_Fasta_get_entry_obtains_the_correct_type
- fasta = Fasta.new(StringIO.new(">test\nATCG\n"), 'DNA')
- assert_equal(fasta.get_entry.type, "dna")
- end
-
- def test_Fasta_get_entry_rstrips_whitespace_from_seq_name
- fasta = Fasta.new(StringIO.new(">test\n\r\t ATCG\n"))
- assert_equal(fasta.get_entry.seq_name, "test")
- end
-
- def test_Fasta_get_entry_strips_whitespace_from_seq
- fasta = Fasta.new(StringIO.new(">test\n\r\t AT\n\r\t CG\n\r\t "))
- assert_equal(fasta.get_entry.seq, "ATCG")
- end
-
- def test_Fasta_get_entry_with_two_entries_obtain_correct
- fasta = Fasta.new(StringIO.new(">test1\n\r\t AT\n\r\t CG\n\r\t \n>test2\n\r\t atcg\n"))
- assert_equal(fasta.get_entry.seq, "ATCG")
- assert_equal(fasta.get_entry.seq, "atcg")
- end
-
- def test_Fasta_get_entry_without_seq_name_raises
- fasta = Fasta.new(StringIO.new("ATCG\n"))
- assert_raise( FastaError ) { fasta.get_entry }
- end
-
- def test_Fasta_get_entry_without_seq_raises
- fasta = Fasta.new(StringIO.new(">test\n\n"))
- assert_raise( FastaError ) { fasta.get_entry }
- end
-
- def test_Fasta_get_entry_with_leading_newline_raises
- fasta = Fasta.new(StringIO.new("\n>test\nATCG\n"))
- assert_raise( FastaError ) { fasta.get_entry }
- end
-
-# FIXME
-# def test_Fasta_get_entry raises on missing > in seq_name
-# fasta = Fasta.new(StringIO.new("test\nATCG\n"))
-# assert_raise( FastaError ) { fasta.get_entry }
-# end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'test/unit'
-require 'fastq'
-require 'stringio'
-require 'pp'
-
-class FastqTest < Test::Unit::TestCase
- def setup
- @io = StringIO.new("@test1\nATCG\n+\nABCD\n@test2\natcg\n+test2\n@ABG\n")
- @fastq = Fastq.new(@io)
- end
-
- def test_Fastq_get_entry_obtains_the_correct_seq_name
- assert_equal("test1", @fastq.get_entry.seq_name)
- end
-
- def test_Fasta_get_entry_obtains_the_correct_type
- fastq = Fastq.new(@io, 'DNA')
- assert_equal("dna", fastq.get_entry.type)
- end
-
- def test_Fastq_get_entry_with_two_entries_obtain_correct
- assert_equal("ATCG", @fastq.get_entry.seq)
- assert_equal("atcg", @fastq.get_entry.seq)
- end
-
- def test_Fastq_each_loop_ends_correctly
- @fastq.each do |entry|
- end
- end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-require 'genbank'
-require 'seq'
-require 'test/unit'
-require 'pp'
-
-class TestGenbank < Test::Unit::TestCase
- def setup
- @seq = Seq.new(nil, "tcatgatcaagatctaacagcagaagtacacttctattta", "dna")
- end
-
- def test_Locator_with_single_position_returns_correctly
- loc = Locator.new("10", @seq)
- assert_equal("a", loc.subseq.seq)
- end
-
- def test_Locator_with_single_interval_returns_correctly
- loc = Locator.new("5..10", @seq)
- assert_equal("gatca", loc.subseq.seq)
- end
-
- def test_Locator_with_multiple_intervals_return_correctly
- loc = Locator.new("5..10,15..20", @seq)
- assert_equal("gatcataaca", loc.subseq.seq)
- end
-
- def test_Locator_with_join_multiple_intervals_return_correctly
- loc = Locator.new("join(5..10,15..20)", @seq)
- assert_equal("gatcataaca", loc.subseq.seq)
- end
-
- def test_Locator_with_complement_and_single_interval_return_correctly
- loc = Locator.new("complement(5..10)", @seq)
- assert_equal("tgatc", loc.subseq.seq)
- end
-end
-
-
-__END__
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-
-# Copyright (C) 2007-2010 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'seq'
-require 'test/unit'
-require 'pp'
-
-class TestPatternMatcher < Test::Unit::TestCase
- def setup
- @p = Seq.new("test", "atcg")
- end
-
- def test_PatternMatcher_no_match_returns_nil
- assert_nil(@p.match("gggg"))
- end
-
- def test_PatternMatcher_match_perfect_returns_correctly
- m = @p.match("atcg")
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(4, m.matches)
- assert_equal(0, m.mismatches)
- assert_equal(0, m.insertions)
- assert_equal(0, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_match_perfect_with_ambiguity_codes_returns_correctly
- m = @p.match("nnnn")
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(4, m.matches)
- assert_equal(0, m.mismatches)
- assert_equal(0, m.insertions)
- assert_equal(0, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_zero_returns_nil
- assert_nil(@p.match("aCcg"))
- end
-
- def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_one_returns_correctly
- m = @p.match("aCcg", pos = 0, edit_distance = 1)
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(3, m.matches)
- assert_equal(1, m.mismatches)
- assert_equal(0, m.insertions)
- assert_equal(0, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_match_with_two_mismatch_and_edit_dist_one_returns_nil
- assert_nil(@p.match("aGcA", pos = 0, edit_distance = 1))
- end
-
- def test_PatternMatcher_match_with_one_insertion_and_edit_dist_zero_returns_nil
- assert_nil(@p.match("atGcg"))
- end
-
- def test_PatternMatcher_match_with_one_insertion_and_edit_dist_one_returns_correctly
- m = @p.match("atGcg", pos = 0, edit_distance = 1)
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(4, m.matches)
- assert_equal(0, m.mismatches)
- assert_equal(1, m.insertions)
- assert_equal(0, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_match_with_two_insertions_and_edit_dist_one_returns_nil
- assert_nil(@p.match("atGcTg", pos = 0, edit_distance = 1))
- end
-
- def test_PatternMatcher_match_with_two_insertions_and_edit_dist_two_returns_correctly
- m = @p.match("atGcTg", pos = 0, edit_distance = 2)
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(4, m.matches)
- assert_equal(0, m.mismatches)
- assert_equal(2, m.insertions)
- assert_equal(0, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_match_with_one_deletion_and_edit_distance_zero_returns_nil
- assert_nil(@p.match("acg"))
- end
-
- def test_PatternMatcher_match_with_one_deletion_and_edit_distance_one_returns_correctly
- m = @p.match("acg", pos = 0, edit_distance = 1)
- assert_equal(0, m.pos)
- assert_equal("atcg", m.match)
- assert_equal(3, m.matches)
- assert_equal(0, m.mismatches)
- assert_equal(0, m.insertions)
- assert_equal(1, m.deletions)
- assert_equal(4, m.length)
- end
-
- def test_PatternMatcher_scan_locates_three_patterns_ok
- p = Seq.new("test", "ataacgagctagctagctagctgactac")
- assert_equal(3, p.scan("tag").count)
- end
-
- def test_PatternMatcher_scan_with_pos_locates_two_patterns_ok
- p = Seq.new("test", "ataacgagctagctagctagctgactac")
- assert_equal(2, p.scan("tag", 10).count)
- end
-end
+++ /dev/null
-#!/usr/bin/env ruby
-
-require 'seq'
-require 'test/unit'
-require 'pp'
-
-class TestSeq < Test::Unit::TestCase
- def setup
- @entry = Seq.new
- end
-
- # def test_Seq# autoremoves whitespace, newlines, and carriage returns
- # dna = Seq.new
- # dna.seq = "A\tT\r\tC\nG "
- # assert_equal(dna.seq, "ATCG")
- # end
-
- def test_Seq_is_dna_with_no_sequence_type_returns_false
- assert(@entry.is_dna? == false)
- end
-
- def test_Seq_is_dna_with_dna_sequence_type_returns_true
- @entry.type = 'dna'
- assert(@entry.is_dna? == true)
- end
-
- def test_Seq_is_rna_with_no_sequence_type_returns_false
- assert(@entry.is_rna? == false)
- end
-
- def test_Seq_is_rna_with_rna_sequence_type_returns_true
- @entry.type = 'rna'
- assert(@entry.is_rna? == true)
- end
-
- def test_Seq_is_protein_with_no_sequence_type_returns_false
- assert(@entry.is_protein? == false)
- end
-
- def test_Seq_is_protein_with_protein_sequence_type_returns_true
- @entry.type = 'protein'
- assert(@entry.is_protein? == true)
- end
-
- def test_Seq_length_is_correct
- @entry.seq = 'ATCG'
- assert_equal(4, @entry.length)
- end
-
- def test_Seq_indels_is_correct
- @entry.seq = 'ATCG.-~_'
- assert_equal(4, @entry.indels)
- end
-
- def test_Seq_to_rna_raises_if_no_sequence
- @entry.type = 'dna'
- assert_raise(SeqError) { @entry.to_rna }
- end
-
- def test_Seq_to_rna_raises_on_bad_type
- @entry.seq = 'ATCG'
- @entry.type = 'rna'
- assert_raise(SeqError) { @entry.to_rna }
- end
-
- def test_Seq_to_rna_transcribes_correctly
- @entry.seq = 'ATCGatcg'
- @entry.type = 'dna'
- assert_equal("AUCGaucg", @entry.to_rna)
- end
-
- def test_Seq_to_rna_changes_entry_type_to_rna
- @entry.seq = 'ATCGatcg'
- @entry.type = 'dna'
- @entry.to_rna
- assert_equal("rna", @entry.type)
- end
-
- def test_Seq_to_dna_raises_if_no_sequence
- @entry.type = 'rna'
- assert_raise(SeqError) { @entry.to_dna }
- end
-
- def test_Seq_to_dna_raises_on_bad_type
- @entry.seq = 'AUCG'
- @entry.type = 'dna'
- assert_raise(SeqError) { @entry.to_dna }
- end
-
- def test_Seq_to_dna_transcribes_correctly
- @entry.seq = 'AUCGaucg'
- @entry.type = 'rna'
- assert_equal("ATCGatcg", @entry.to_dna)
- end
-
- def test_Seq_to_dna_changes_entry_type_to_dna
- @entry.seq = 'AUCGaucg'
- @entry.type = 'rna'
- @entry.to_dna
- assert_equal("dna", @entry.type)
- end
-
- def test_Seq_to_bp_returns_correct_record
- @entry.seq_name = 'test'
- @entry.seq = 'ATCG'
- assert_equal({:SEQ_NAME=>"test", :SEQ=>"ATCG", :SEQ_LEN=>4}, @entry.to_bp)
- end
-
- def test_Seq_to_bp_raises_on_missing_seq_name
- @entry.seq = 'ATCG'
- assert_raise(SeqError) { @entry.to_bp }
- end
-
- def test_Seq_to_bp_raises_on_missing_sequence
- @entry.seq_name = 'test'
- assert_raise(SeqError) { @entry.to_bp }
- end
-
- def test_Seq_to_fasta_returns_correct_entry
- @entry.seq_name = 'test'
- @entry.seq = 'ATCG'
- assert_equal(">test\nATCG\n", @entry.to_fasta)
- end
-
- def test_Seq_to_fasta_wraps_correctly
- entry = Seq.new("test", "ATCG")
- assert_equal(">test\nAT\nCG\n", entry.to_fasta(2))
- end
-
- def test_Seq_to_key_with_bad_residue_raises
- entry = Seq.new("test", "AUCG")
- assert_raise(SeqError) { entry.to_key }
- end
-
- def test_Seq_to_key_returns_correctly
- entry = Seq.new("test", "ATCG")
- assert_equal(54, entry.to_key)
- end
-
- def test_Seq_reverse_returns_correctly
- @entry.seq = "ATCG"
- assert_equal("GCTA", @entry.reverse)
- end
-
- def test_Seq_complement_raises_if_no_sequence
- @entry.type = 'dna'
- assert_raise(SeqError) { @entry.complement }
- end
-
- def test_Seq_complement_raises_on_bad_type
- @entry.seq = 'ATCG'
- @entry.type = 'protein'
- assert_raise(SeqError) { @entry.complement }
- end
-
- def test_Seq_complement_for_DNA_is_correct
- @entry.seq = 'ATCGatcg'
- @entry.type = 'dna'
- assert_equal("TAGCtagc", @entry.complement)
- end
-
- def test_Seq_complement_for_RNA_is_correct
- @entry.seq = 'AUCGaucg'
- @entry.type = 'rna'
- assert_equal("UAGCuagc", @entry.complement)
- end
-
- def test_Seq_reverse_complement_for_DNA_is_correct
- @entry.seq = 'ATCGatcg'
- @entry.type = 'dna'
- assert_equal("cgatCGAT", @entry.reverse_complement)
- end
-
- def test_Seq_reverse_complement_for_RNA_is_correct
- @entry.seq = 'AUCGaucg'
- @entry.type = 'rna'
- assert_equal("cgauCGAU", @entry.reverse_complement)
- end
-
- def test_Seq_generate_with_length_lt_1_raises
- assert_raise(SeqError) { @entry.generate(-10, "dna") }
- assert_raise(SeqError) { @entry.generate(0, "dna") }
- end
-
- def test_Seq_generate_with_bad_type_raises
- assert_raise(SeqError) { @entry.generate(10, "foo") }
- end
-
- def test_Seq_generate_with_ok_type_dont_raise
- %w[dna DNA rna RNA protein Protein].each do |type|
- assert_nothing_raised { @entry.generate(10, type) }
- end
- end
-
- def test_Seq_subseq_with_start_lt_0_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq(-1, 1) }
- end
-
- def test_Seq_subseq_with_length_lt_1_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq(0, 0) }
- end
-
- def test_Seq_subseq_with_start_plus_length_gt_seq_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq(0, 5) }
- end
-
- def test_Seq_subseq_returns_correct_sequence
- @entry.seq = "ATCG"
- assert_equal("AT", @entry.subseq(0, 2).seq)
- assert_equal("CG", @entry.subseq(2, 2).seq)
- end
-
- def test_Seq_subseq_without_len_returns_correct_sequence
- @entry.seq = "ATCG"
- assert_equal("ATCG", @entry.subseq(0).seq)
- assert_equal("CG", @entry.subseq(2).seq)
- end
-
- def test_Seq_subseq_returns_correct_qual
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- assert_equal("ab", @entry.subseq(0, 2).qual)
- assert_equal("cd", @entry.subseq(2, 2).qual)
- end
-
- def test_Seq_subseq_without_len_returns_correct_qual
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- assert_equal("abcd", @entry.subseq(0).qual)
- assert_equal("cd", @entry.subseq(2).qual)
- end
-
- def test_Seq_subseq_bang_with_start_lt_0_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq!(-1, 1) }
- end
-
- def test_Seq_subseq_bang_with_length_lt_1_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq!(0, 0) }
- end
-
- def test_Seq_subseq_bang_with_start_plus_length_gt_seq_raises
- @entry.seq = "ATCG"
- assert_raise(SeqError) { @entry.subseq!(0, 5) }
- end
-
- def test_Seq_subseq_bang_returns_correct_sequence
- @entry.seq = "ATCG"
- @entry.subseq!(0, 2)
- assert_equal("AT", @entry.seq)
- @entry.seq = "ATCG"
- @entry.subseq!(2, 2)
- assert_equal("CG", @entry.seq)
- end
-
- def test_Seq_subseq_bang_without_len_returns_correct_sequence
- @entry.seq = "ATCG"
- @entry.subseq!(0)
- assert_equal("ATCG", @entry.seq)
- @entry.seq = "ATCG"
- @entry.subseq!(2)
- assert_equal("CG", @entry.seq)
- end
-
- def test_Seq_subseq_bang_with_pos_and_len_returns_correct_qual
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- @entry.subseq!(0, 2)
- assert_equal("ab", @entry.qual)
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- @entry.subseq!(2, 2)
- assert_equal("cd", @entry.qual)
- end
-
- def test_Seq_subseq_bang_with_pos_returns_correct_qual
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- @entry.subseq!(0)
- assert_equal("abcd", @entry.qual)
- @entry.seq = "ATCG"
- @entry.qual = "abcd"
- @entry.subseq!(2)
- assert_equal("cd", @entry.qual)
- end
-
- def test_Seq_subseq_rand_returns_correct_sequence
- @entry.seq = "ATCG"
- assert_equal("ATCG", @entry.subseq_rand(4).seq)
- end
-
- def test_Seq_composition_returns_correctly
- @entry.seq = "AAAATTTCCG"
- assert_equal(4, @entry.composition["A"])
- assert_equal(3, @entry.composition["T"])
- assert_equal(2, @entry.composition["C"])
- assert_equal(1, @entry.composition["G"])
- assert_equal(0, @entry.composition["X"])
- end
-
- def test_Seq_homopol_max_returns_0_with_empty_sequence
- @entry.seq = ""
- assert_equal(0, @entry.homopol_max)
- end
-
- def test_Seq_homopol_max_returns_0_with_nil_sequence
- @entry.seq = nil
- assert_equal(0, @entry.homopol_max)
- end
-
- def test_Seq_homopol_max_returns_0_when_not_found
- @entry.seq = "AtTcCcGggGnnNnn"
- assert_equal(0, @entry.homopol_max(6))
- end
-
- def test_Seq_homopol_max_returns_correctly
- @entry.seq = "AtTcCcGggGnnNnn"
- assert_equal(5, @entry.homopol_max(3))
- end
-
- def test_Seq_hard_mask_returns_correctly
- @entry.seq = "--AAAANn"
- assert_equal(33.33, @entry.hard_mask)
- end
-
- def test_Seq_soft_mask_returns_correctly
- @entry.seq = "--AAAa"
- assert_equal(25.00, @entry.soft_mask)
- end
-end
-
-
-__END__
+++ /dev/null
-class Test
- puts "Modules Test2 loaded"
-
- def greet_world
- puts "World"
- end
-end
--- /dev/null
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Error class for all exceptions to do with Base36.
+class Base36Error < StandardError; end
+
+ALPH = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
+BASE36 = 36
+
+# Class containing methods to encode and decode Base 36.
+# Note that the ALPH is [alph + num] and not [num + alph]
+# which prevents us from simply using .to_i(36) and .to_s(36).
+#
+# http://en.wikipedia.org/wiki/Base_36
+class Base36
+ # Method that encodes an integer into a base36 string
+ # that is returned.
+ def self.encode(num)
+ raise Base36Error unless num.is_a? Fixnum
+
+ base36 = ""
+
+ while num > 0
+ base36 << ALPH[(num % BASE36)]
+ num /= BASE36
+ end
+
+ base36 << ALPH[0] if num == 0
+
+ base36.reverse
+ end
+
+ # Method that decodes a base36 string and returns an integer.
+ def self.decode(base36)
+ raise Base36Error if base36.empty?
+
+ result = 0
+ pos = 0
+
+ base36.upcase.reverse.each_char do |char|
+ result += ALPH.index(char) * (BASE36 ** pos)
+ pos += 1
+ end
+
+ return result;
+ end
+end
+
+__END__
--- /dev/null
+raise "Ruby 1.9 or later required" if RUBY_VERSION < "1.9"
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'fileutils'
+require 'date'
+require 'optparse'
+require 'open3'
+require 'pp'
+
+# Biopieces are command line scripts and uses OptionParser to parse command line
+# options according to a list of casts. Each cast prescribes the long and short
+# name of the option, the type, if it is mandatory, the default value, and allowed
+# and disallowed values. An optional list of extra casts can be supplied, and the
+# integrity of the casts are checked. Following the command line parsing, the
+# options are checked according to the casts. Methods are also included for handling
+# the parsing and emitting of Biopiece records, which are ASCII text records consisting
+# of lines with a key/value pair separated by a colon and a white space ': '.
+# Each record is separated by a line with three dashes '---'.
+class Biopieces
+ include Enumerable
+
+ attr_accessor :out # accessor for out stream _ios_
+
+ # Initialize a Biopiece and write the status to file.
+ # Options are for testing purposes only.
+ def initialize(test=nil, input=STDIN, output=STDOUT)
+ @test = test
+ @input = input
+ @output = output
+ end
+
+ # Check the integrity of a list of casts, followed by parsion options from argv
+ # and finally checking the options according to the casts. Returns nil if argv
+ # is empty, otherwise an options hash.
+ def parse(argv, cast_list=[], script_path=$0)
+ casts = Casts.new(cast_list)
+ option_handler = OptionHandler.new(argv, casts, script_path, @test)
+ @options = option_handler.options_parse
+ end
+
+ # Open Biopiece input stream if not open and iterate over all Biopiece
+ # records in the stream.
+ def each_record
+ @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
+ return if @in.nil?
+
+ record = {}
+
+ @in.each_line do |line|
+ case line
+ when /^([^:]+): (.*)$/
+ record[$1.to_sym] = $2
+ when /^---$/
+ yield record unless record.empty?
+ record = {}
+ else
+ raise "Bad record format: #{line}"
+ end
+ end
+
+ yield record unless record.empty?
+
+ self # conventionally
+ end
+
+ alias :each :each_record
+
+ # Open Biopiece output stream if not open and puts record to the stream.
+ def puts(record)
+ @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
+
+ record.each do |key,value|
+ @out.print "#{key.to_s}: #{value}\n"
+ end
+
+ @out.print "---\n"
+ end
+
+ def to_s
+ end
+
+ # Create a temporary directory inside the ENV["BP_TMP"] dir.
+ def mktmpdir
+ time = Time.now.to_i
+ user = ENV["USER"]
+ pid = $$
+ path = ENV["BP_TMP"] + "/" + [user, time + pid, pid, "bp_tmp"].join("_")
+ Dir.mkdir(path)
+ Status.new.set_tmpdir(path)
+ path
+ end
+end
+
+
+# Error class for all exceptions to do with option casts.
+class CastError < StandardError; end
+
+
+# Class to handle casts of command line options. Each cast prescribes the long and
+# short name of the option, the type, if it is mandatory, the default value, and
+# allowed and disallowed values. An optional list of extra casts can be supplied,
+# and the integrity of the casts are checked.
+class Casts < Array
+ TYPES = %w[flag string list int uint float file file! files files! dir dir! genome]
+ MANDATORY = %w[long short type mandatory default allowed disallowed]
+
+ # Initialize cast object with an optional options cast list to which
+ # ubiquitous casts are added after which all casts are checked.
+ def initialize(cast_list=[])
+ @cast_list = cast_list
+ ubiquitous
+ check
+ long_to_sym
+ self.push(*@cast_list)
+ end
+
+ private
+
+ # Add ubiquitous options casts.
+ def ubiquitous
+ @cast_list << {:long=>'help', :short=>'?', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ @cast_list << {:long=>'stream_in', :short=>'I', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ @cast_list << {:long=>'stream_out', :short=>'O', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ @cast_list << {:long=>'verbose', :short=>'v', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ end
+
+ # Check integrity of the casts.
+ def check
+ check_keys
+ check_values
+ check_duplicates
+ end
+
+ # Check if all mandatory keys are present in casts and raise if not.
+ def check_keys
+ @cast_list.each do |cast|
+ MANDATORY.each do |mandatory|
+ raise CastError, "Missing symbol in cast: '#{mandatory.to_sym}'" unless cast.has_key? mandatory.to_sym
+ end
+ end
+ end
+
+ # Check if all values in casts are valid.
+ def check_values
+ @cast_list.each do |cast|
+ check_val_long(cast)
+ check_val_short(cast)
+ check_val_type(cast)
+ check_val_mandatory(cast)
+ check_val_default(cast)
+ check_val_allowed(cast)
+ check_val_disallowed(cast)
+ end
+ end
+
+ # Check if the values to long are legal and raise if not.
+ def check_val_long(cast)
+ unless cast[:long].is_a? String and cast[:long].length > 1
+ raise CastError, "Illegal cast of long: '#{cast[:long]}'"
+ end
+ end
+
+ # Check if the values to short are legal and raise if not.
+ def check_val_short(cast)
+ unless cast[:short].is_a? String and cast[:short].length == 1
+ raise CastError, "Illegal cast of short: '#{cast[:short]}'"
+ end
+ end
+
+ # Check if values to type are legal and raise if not.
+ def check_val_type(cast)
+ type_hash = {}
+ TYPES.each do |type|
+ type_hash[type] = true
+ end
+
+ unless type_hash.has_key? cast[:type]
+ raise CastError, "Illegal cast of type: '#{cast[:type]}'"
+ end
+ end
+
+ # Check if values to mandatory are legal and raise if not.
+ def check_val_mandatory(cast)
+ unless cast[:mandatory] == true or cast[:mandatory] == false
+ raise CastError, "Illegal cast of mandatory: '#{cast[:mandatory]}'"
+ end
+ end
+
+ # Check if values to default are legal and raise if not.
+ def check_val_default(cast)
+ unless cast[:default].nil? or
+ cast[:default].is_a? String or
+ cast[:default].is_a? Integer or
+ cast[:default].is_a? Float
+ raise CastError, "Illegal cast of default: '#{cast[:default]}'"
+ end
+ end
+
+ # Check if values to allowed are legal and raise if not.
+ def check_val_allowed(cast)
+ unless cast[:allowed].is_a? String or cast[:allowed].nil?
+ raise CastError, "Illegal cast of allowed: '#{cast[:allowed]}'"
+ end
+ end
+
+ # Check if values to disallowed are legal and raise if not.
+ def check_val_disallowed(cast)
+ unless cast[:disallowed].is_a? String or cast[:disallowed].nil?
+ raise CastError, "Illegal cast of disallowed: '#{cast[:disallowed]}'"
+ end
+ end
+
+ # Check cast for duplicate long or short options names.
+ def check_duplicates
+ check_hash = {}
+ @cast_list.each do |cast|
+ raise CastError, "Duplicate argument: '--#{cast[:long]}'" if check_hash.has_key? cast[:long]
+ raise CastError, "Duplicate argument: '-#{cast[:short]}'" if check_hash.has_key? cast[:short]
+ check_hash[cast[:long]] = true
+ check_hash[cast[:short]] = true
+ end
+ end
+
+ # Convert values to :long keys to symbols for all casts.
+ def long_to_sym
+ @cast_list.each do |cast|
+ cast[:long] = cast[:long].to_sym
+ end
+ end
+
+end
+
+
+# Class for parsing argv using OptionParser according to given casts.
+# Default options are set, file glob expressions expanded, and options are
+# checked according to the casts. Usage information is printed and exit called
+# if required.
+class OptionHandler
+ REGEX_LIST = /^(list|files|files!)$/
+ REGEX_INT = /^(int|uint)$/
+ REGEX_STRING = /^(file|file!|dir|dir!|genome)$/
+
+ def initialize(argv, casts, script_path, test=nil)
+ @argv = argv
+ @casts = casts
+ @script_path = script_path
+ @test = test
+ end
+
+ # Parse options from argv using OptionParser and casts denoting long and
+ # short option names. Usage information is printed and exit called.
+ # A hash with options is returned.
+ def options_parse
+ @options = {}
+
+ option_parser = OptionParser.new do |option|
+ @casts.each do |cast|
+ case cast[:type]
+ when 'flag'
+ option.on("-#{cast[:short]}", "--#{cast[:long]}") do |o|
+ @options[cast[:long]] = o
+ end
+ when 'float'
+ option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
+ @options[cast[:long]] = f
+ end
+ when 'string'
+ option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+ @options[cast[:long]] = s.to_sym # TODO: this to_sym - is that needed?
+ end
+ when REGEX_LIST
+ option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
+ @options[cast[:long]] = a
+ end
+ when REGEX_INT
+ option.on("-#{cast[:short]}", "--#{cast[:long]} I", Integer) do |i|
+ @options[cast[:long]] = i
+ end
+ when REGEX_STRING
+ option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
+ @options[cast[:long]] = s
+ end
+ else
+ raise ArgumentError, "Unknown option type: '#{cast[:type]}'"
+ end
+ end
+ end
+
+ option_parser.parse!(@argv)
+
+ if print_usage_full?
+ print_usage_and_exit(true)
+ elsif print_usage_short?
+ print_usage_and_exit
+ end
+
+ options_default
+ options_glob
+ options_check
+
+ @options
+ end
+
+ # Given the script name determine the path of the wiki file with the usage info.
+ def wiki_path
+ path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
+ raise "No such wiki file: #{path}" unless File.file? path
+ path
+ end
+
+ # Check if full "usage info" should be printed.
+ def print_usage_full?
+ @options[:help]
+ end
+
+ # Check if short "usage info" should be printed.
+ def print_usage_short?
+ if not $stdin.tty?
+ return false
+ elsif @options[:stream_in]
+ return false
+ elsif @options[:data_in]
+ return false
+ elsif wiki_path =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/ # TODO get rid of this!
+ return false
+ else
+ return true
+ end
+ end
+
+ # Print usage info by Calling an external script 'print_wiki'
+ # using a system() call and exit. An optional 'full' flag
+ # outputs the full usage info.
+ def print_usage_and_exit(full=nil)
+ if @test
+ return
+ else
+ if full
+ system("print_wiki --data_in #{wiki_path} --help")
+ else
+ system("print_wiki --data_in #{wiki_path}")
+ end
+
+ raise "Failed printing wiki: #{wiki_path}" unless $?.success?
+
+ exit
+ end
+ end
+
+ # Set default options value from cast unless a value is set.
+ def options_default
+ @casts.each do |cast|
+ if cast[:default]
+ unless @options.has_key? cast[:long]
+ if cast[:type] == 'list'
+ @options[cast[:long]] = cast[:default].split ','
+ else
+ @options[cast[:long]] = cast[:default]
+ end
+ end
+ end
+ end
+ end
+
+ # Expands glob expressions to a full list of paths.
+ # Examples: "*.fna" or "foo.fna,*.fna" or "foo.fna,/bar/*.fna"
+ def options_glob
+ @casts.each do |cast|
+ if cast[:type] == 'files' or cast[:type] == 'files!'
+ if @options.has_key? cast[:long]
+ files = []
+
+ @options[cast[:long]].each do |path|
+ if path.include? "*"
+ Dir.glob(path).each do |file|
+ files << file if File.file? file
+ end
+ else
+ files << path
+ end
+ end
+
+ @options[cast[:long]] = files
+ end
+ end
+ end
+ end
+
+ # Check all options according to casts.
+ def options_check
+ @casts.each do |cast|
+ options_check_mandatory(cast)
+ options_check_int(cast)
+ options_check_uint(cast)
+ options_check_file(cast)
+ options_check_files(cast)
+ options_check_dir(cast)
+ options_check_allowed(cast)
+ options_check_disallowed(cast)
+ end
+ end
+
+ # Check if a mandatory option is set and raise if it isn't.
+ def options_check_mandatory(cast)
+ if cast[:mandatory]
+ raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
+ end
+ end
+
+ # Check int type option and raise if not an integer.
+ def options_check_int(cast)
+ if cast[:type] == 'int' and @options.has_key? cast[:long]
+ unless @options[cast[:long]].is_a? Integer
+ raise ArgumentError, "Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"
+ end
+ end
+ end
+
+ # Check uint type option and raise if not an unsinged integer.
+ def options_check_uint(cast)
+ if cast[:type] == 'uint' and @options.has_key? cast[:long]
+ unless @options[cast[:long]].is_a? Integer and @options[cast[:long]] >= 0
+ raise ArgumentError, "Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"
+ end
+ end
+ end
+
+ # Check file! type argument and raise if file don't exists.
+ def options_check_file(cast)
+ if cast[:type] == 'file!' and @options.has_key? cast[:long]
+ raise ArgumentError, "No such file: '#{@options[cast[:long]]}'" unless File.file? @options[cast[:long]]
+ end
+ end
+
+ # Check files! type argument and raise if files don't exists.
+ def options_check_files(cast)
+ if cast[:type] == 'files!' and @options.has_key? cast[:long]
+ @options[cast[:long]].each do |path|
+ next if path == "-"
+ raise ArgumentError, "File not readable: '#{path}'" unless File.readable? path
+ end
+ end
+ end
+
+ # Check dir! type argument and raise if directory don't exist.
+ def options_check_dir(cast)
+ if cast[:type] == 'dir!' and @options.has_key? cast[:long]
+ raise ArgumentError, "No such directory: '#{@options[cast[:long]]}'" unless File.directory? @options[cast[:long]]
+ end
+ end
+
+ # Check options and raise unless allowed.
+ def options_check_allowed(cast)
+ if cast[:allowed] and @options.has_key? cast[:long]
+ allowed_hash = {}
+ cast[:allowed].split(',').each { |a| allowed_hash[a.to_s] = 1 }
+
+ raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed" unless allowed_hash.has_key? @options[cast[:long]].to_s
+ end
+ end
+
+ # Check disallowed argument values and raise if disallowed.
+ def options_check_disallowed(cast)
+ if cast[:disallowed] and @options.has_key? cast[:long]
+ cast[:disallowed].split(',').each do |val|
+ raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed" if val.to_s == @options[cast[:long]].to_s
+ end
+ end
+ end
+end
+
+# Class for manipulating the execution status of Biopieces by setting a
+# status file with a time stamp, process id, and command arguments. The
+# status file is used for creating log entries and for displaying the
+# runtime status of Biopieces.
+class Status
+ # Write the status to a status file.
+ def set
+ time0 = Time.new.strftime("%Y-%m-%d %X")
+
+ File.open(path, mode="w") do |fh|
+ fh.puts [time0, ARGV.join(" ")].join(";")
+ end
+ end
+
+ # Append the a temporary directory path to the status file.
+ def set_tmpdir(tmpdir_path)
+ status = ""
+
+ File.open(path, mode="r") do |fh|
+ status = fh.read.chomp
+ end
+
+ status = "#{status};#{tmpdir_path}\n"
+
+ File.open(path, mode="w") do |fh|
+ fh << status
+ end
+ end
+
+ # Extract the temporary directory path from the status file,
+ # and return this or nil if not found.
+ def get_tmpdir
+ File.open(path, mode="r") do |fh|
+ tmpdir_path = fh.read.chomp.split(";").last
+ return tmpdir_path if File.directory?(tmpdir_path)
+ end
+
+ nil
+ end
+
+ # Write the Biopiece status to the log file.
+ def log(exit_status)
+ time1 = Time.new.strftime("%Y-%m-%d %X")
+ user = ENV["USER"]
+ script = File.basename($0)
+
+ stream = File.open(path)
+ time0, args, tmp_dir = stream.first.split(";")
+ stream.close
+
+ elap = time_diff(time0, time1)
+ command = [script, args].join(" ")
+ log_file = ENV["BP_LOG"] + "/biopieces.log"
+
+ File.open(log_file, mode = "a") { |file| file.puts [time0, time1, elap, user, exit_status, command].join("\t") }
+ end
+
+ # Delete status file.
+ def delete
+ File.delete(path)
+ end
+
+ private
+
+ # Path to status file
+ def path
+ user = ENV["USER"]
+ script = File.basename($0)
+ pid = $$
+ path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
+ end
+
+ # Get the elapsed time from the difference between two time stamps.
+ def time_diff(t0, t1)
+ Time.at((DateTime.parse(t1).to_time - DateTime.parse(t0).to_time).to_i).gmtime.strftime('%X')
+ end
+end
+
+
+class Stream < IO
+ # Open Biopieces output data stream for reading from stdin or a file
+ # specified in options[:stream_in] OR writing to stdout or a file
+ # specified in options[:stream_out] or options[:data_out].
+ def self.open(options, mode, stdio)
+ if mode == "r"
+ if options[:data_in] and options[:data_in].first == "-"
+ self.nread(["-"])
+ else
+ $stdin.tty? ? read(options[:stream_in]) : stdio
+ end
+ elsif mode == "w"
+ options[:stream_out] ? self.write(options[:stream_out], options[:compress]) : stdio
+ else
+ raise "Bad mode #{mode}"
+ end
+ end
+
+ private
+
+ # Opens a reads stream to a list of files.
+ def self.read(files)
+ return if files.nil? #TODO case/when
+ self.zipped?(files) ? self.zread(files) : self.nread(files)
+ end
+
+ # Opens a write stream to a file and returns a _io_ object.
+ def self.write(file, zip=nil)
+ zip ? self.zwrite(file) : self.nwrite(file)
+ end
+
+ # Opens a list of gzipped files for reading and return an _io_ object.
+ def self.zread(files)
+ stdin, stdout, stderr = Open3.popen3("zcat " + files.join(' '));
+ stdin.close
+ stderr.close
+ stdout
+ end
+
+ # Opens a file for gzipped writing and return an _io_ object.
+ def self.zwrite(file)
+ stdin, stdout, stderr = Open3.popen3("gzip -f > #{file}")
+ stderr.close
+ stdout.close
+ stdin
+ end
+
+ # Opens a list of files for reading and return an _io_ object.
+ def self.nread(files)
+ stdin, stdout, stderr = Open3.popen3("cat " + files.join(' '));
+ stdin.close
+ stderr.close
+ stdout
+ end
+
+ # Opens a file for writing and return an _io_ object.
+ def self.nwrite(file)
+ File.open(file, mode="w")
+ end
+
+ # Test if a list of files are gzipped or not.
+ # Raises if files are mixed zipped and unzipped.
+ def self.zipped?(files)
+ type_hash = {}
+
+ files.each do |file|
+ type = `file #{file}`
+
+ if type =~ /gzip compressed/
+ type_hash[:gzip] = true
+ else
+ type_hash[:ascii] = true
+ end
+ end
+
+ raise "Mixture of zipped and unzipped files" if type_hash.size == 2
+
+ type_hash[:gzip]
+ end
+end
+
+
+Status.new.set
+
+at_exit do
+ exit_status = $! ? $!.inspect : "OK"
+
+ case exit_status
+ when /error|errno/i
+ exit_status = "ERROR"
+ when "Interrupt"
+ exit_status = "INTERRUPTED"
+ when /SIGTERM/
+ exit_status = "TERMINATED"
+ when /SIGQUIT/
+ exit_status = "QUIT"
+ end
+
+ status = Status.new
+ tmpdir = status.get_tmpdir
+ FileUtils.remove_entry_secure(tmpdir) unless tmpdir.nil?
+ status.log(exit_status)
+ status.delete
+end
+
+
+__END__
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+BitsInChar = 8
+
+# Error class for all exceptions to do with BitArray.
+class BitArrayError < StandardError; end
+
+# Class containing methods for creating and manipulating a bit array.
+class BitArray
+ attr_reader :size, :byte_array
+
+ # Method to initialize a new bit array of a given size.
+ def initialize(size)
+ @size = size
+ @byte_array = init_byte_array
+ @count_array = init_count_array
+ end
+
+ # Method to set a bit to 1 at a given position in the bit array.
+ def bit_set(pos)
+ raise BitArrayError, "Position #{pos} must be an integer." unless pos.is_a? Fixnum
+ raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
+
+ @byte_array[byte_pos(pos)] = (@byte_array[byte_pos(pos)].ord | bit_pos(pos)).chr
+ end
+
+ # Method to check if a bit at a given position in the bit array is set.
+ def bit_set?(pos)
+ raise BitArrayError, "Position #{pos} must be an integer." unless pos.is_a? Fixnum
+ raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
+
+ (@byte_array[byte_pos(pos)].ord & bit_pos(pos)) != 0
+ end
+
+ # Method that returns the number of bits set "on" in a bit array.
+ def bits_on
+ bits_on = 0
+
+ (0 ... self.byte_array.size).each do |byte|
+ bits_on += @count_array[self.byte_array[byte].ord]
+ end
+
+ bits_on
+ end
+
+ # Method that returns the number of bits set "off" in a bit array.
+ def bits_off
+ @size - bits_on
+ end
+
+ # Method to run bitwise AND (&) on two bit arrays and return the
+ # result in a new bit array. Bits are copied if they exists in BOTH operands.
+ # 00111100 & 00001101 = 00001100
+ def &(ba)
+ raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+
+ result = BitArray.new(ba.size)
+
+ (0 ... ba.byte_array.size).each do |byte|
+ result.byte_array[byte] = (self.byte_array[byte].ord & ba.byte_array[byte].ord).chr
+ end
+
+ result
+ end
+
+ # Method to run bitwise OR (|) on two bit arrays and return the
+ # result in a new bit array. Bits are copied if they exists in EITHER operands.
+ # 00111100 | 00001101 = 00111101
+ def |(ba)
+ raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+
+ result = BitArray.new(ba.size)
+
+ (0 ... ba.byte_array.size).each do |byte|
+ result.byte_array[byte] = (self.byte_array[byte].ord | ba.byte_array[byte].ord).chr
+ end
+
+ result
+ end
+
+ # Method to run bitwise XOR (^) on two bit arrays and return the
+ # result in a new bit array. Bits are copied if they exists in ONE BUT NOT BOTH operands.
+ # 00111100 ^ 00001101 = 00110001
+ def ^(ba)
+ raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
+
+ result = BitArray.new(ba.size)
+
+ (0 ... ba.byte_array.size).each do |byte|
+ result.byte_array[byte] = (self.byte_array[byte].ord ^ ba.byte_array[byte].ord).chr
+ end
+
+ result
+ end
+
+ # Method to convert a bit array to a string.
+ def to_s
+ string = ""
+
+ (0 ... @size).each do |pos|
+ if self.bit_set? pos
+ string << "1"
+ else
+ string << "0"
+ end
+ end
+
+ string
+ end
+
+ alias :to_string :to_s
+
+ private
+
+ # Method to initialize the byte array (string) that constitutes the bit array.
+ def init_byte_array
+ raise BitArrayError, "Size must be an integer, not #{@size}" unless @size.is_a? Fixnum
+ raise BitArrayError, "Size must be positive, not #{@size}" unless @size > 0
+
+ byte_array = ""
+ byte_array << 0.chr * (((@size - 1) / BitsInChar) + 1)
+
+ byte_array
+ end
+
+ # Method that returns an array where the element index value is
+ # the number of bits set for that index value.
+ def init_count_array
+ count_array = []
+
+ (0 ... (2 ** BitsInChar)).each do |i|
+ count_array << bits_in_char(i)
+ end
+
+ count_array
+ end
+
+ # Method that returns the number of set bits in a char.
+ def bits_in_char(char)
+ bits = 0
+
+ (0 ... BitsInChar).each do |pos|
+ bits += 1 if ((char & bit_pos(pos)) != 0)
+ end
+
+ bits
+ end
+
+ # Method that returns the byte position in the byte array for a given bit position.
+ def byte_pos(pos)
+ pos / BitsInChar
+ end
+
+ # Method that returns the bit position in a byte.
+ def bit_pos(pos)
+ 1 << (BitsInChar - 1 - (pos % BitsInChar))
+ end
+end
+
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Error class for all exceptions to do with String.
+class StringError < StandardError; end
+
+# Monkey patching Class String to add bitwise operators.
+# Behaviour matching Perl's:
+# http://perldoc.perl.org/perlop.html#Bitwise-String-Operators
+class String
+ # Method to that returns the case senstive Hamming Distance between two strings.
+ # http://en.wikipedia.org/wiki/Hamming_distance
+ def self.hamming_dist(str1, str2)
+ raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}" if str1.length != str2.length
+ (str1 ^ str2 ).count("\x01-\xff")
+ end
+
+ # Method that performs bitwise AND operation where bits
+ # are copied if they exists in BOTH operands. If the operand
+ # sizes are different, the & operator methods acts as though
+ # the longer operand were truncated to the length of the shorter.
+ def &(str)
+ new = ""
+
+ (0 ... [self.length, str.length].min).each do |i|
+ new << (self[i].ord & str[i].ord)
+ end
+
+ new
+ end
+
+ # Method that performs bitwise OR operation where bits
+ # are copied if they exists in EITHER operands. If the operand
+ # sizes differ, the shorter operand is extended with the terminal
+ # part of the longer operand.
+ def |(str)
+ new = ""
+
+ min = [self.length, str.length].min
+
+ (0 ... min).each do |i|
+ new << (self[i].ord | str[i].ord)
+ end
+
+ if self.length > str.length
+ new << self[min ... self.length]
+ elsif self.length < str.length
+ new << str[min ... str.length]
+ end
+
+ new
+ end
+
+ # Method that performs bitwise XOR operation where bits
+ # are copied if they exists in ONE BUT NOT BOTH operands.
+ def ^(str)
+ new = ""
+
+ (0 ... [self.length, str.length].min).each do |i|
+ new << (self[i].ord ^ str[i].ord)
+ end
+
+ new
+ end
+end
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/filesys'
+
+# Error class for all exceptions to do with Boulder.
+class BoulderError < StandardError; end
+
+# Record seperator
+SEP = "\n=\n"
+
+# Class to manipulate boulder records - Lincoln Steins own
+# YAML like format:
+# http://stein.cshl.org/boulder/docs/Boulder.html
+class Boulder < Filesys
+ # Initialize a Boulder object.
+ # Options are for testing purposes only.
+ def initialize(input=STDIN, output=STDOUT)
+ @input = input
+ @output = output
+ end
+
+ def each
+ while not @input.eof? do
+ block = @input.gets(SEP)
+ raise BoulderError, "Missing record seperator" unless block =~ /#{SEP}$/
+
+ record = {}
+
+ block.chomp(SEP).each_line do |line|
+ key, val = line.chomp.split('=', 2)
+
+ raise BoulderError, "Missing key/value seperator" if val.nil?
+ raise BoulderError, "Missing key" if key.empty?
+ raise BoulderError, "Missing value" if val.empty?
+
+ record[key.to_sym] = val
+ end
+
+ yield record
+ end
+ end
+
+ # Method that converts and returns a hash record as
+ # a Boulder string.
+ def to_boulder(record)
+ str = ""
+
+ record.each_pair do |key, val|
+ str << "#{key}=#{val}\n"
+ end
+
+ str << "=\n"
+
+ str
+ end
+end
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Error class for all exceptions to do with Digest.
+class DigestError < StandardError; end
+
+class Digest
+ include Enumerable
+
+ # Initialize a digest object with the following arguments:
+ # - seq: A sequence object.
+ # - pattern: A restriction enzyme recognition pattern.
+ # - cut_pos: Offset from match position where the enzyme cuts.
+ def initialize(seq, pattern, cut_pos)
+ @seq = seq
+ @pattern = disambiguate(pattern)
+ @cut_pos = cut_pos
+ @offset = 0
+ end
+
+ # Method to get the next digestion product from a sequence.
+ def each
+ @seq.seq.upcase.scan @pattern do
+ pos = $`.length + @cut_pos - 1
+
+ if pos >= 0 and pos < @seq.length - 2
+ seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{pos}]", @seq.seq[@offset .. pos], @seq.type)
+
+ yield seq
+ end
+
+ @offset = pos + 1
+ end
+
+ if @offset < 0
+ @offset = 0
+ elsif @offset > @seq.length
+ @offset = 0
+ end
+
+ seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]", @seq.seq[@offset .. @seq.length], @seq.type)
+
+ yield seq
+
+ self # conventionally
+ end
+
+ private
+
+ # Method that returns a regexp object with a restriction
+ # enzyme pattern with ambiguity codes substituted to the
+ # appropriate regexp.
+ def disambiguate(pattern)
+ ambiguity = {
+ 'A' => "A",
+ 'T' => "T",
+ 'U' => "T",
+ 'C' => "C",
+ 'G' => "G",
+ 'M' => "[AC]",
+ 'R' => "[AG]",
+ 'W' => "[AT]",
+ 'S' => "[CG]",
+ 'Y' => "[CT]",
+ 'K' => "[GT]",
+ 'V' => "[ACG]",
+ 'H' => "[ACT]",
+ 'D' => "[AGT]",
+ 'B' => "[CGT]",
+ 'N' => "[GATC]"
+ }
+
+ new_pattern = ""
+
+ pattern.upcase.each_char do |char|
+ if ambiguity.has_key? char
+ new_pattern << ambiguity[char]
+ else
+ raise DigestError, "Could not disambiguate residue: #{char}"
+ end
+ end
+
+ Regexp.new(new_pattern)
+ end
+end
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/seq'
+require 'maasha/filesys'
+
+# Error class for all exceptions to do with FASTA.
+class FastaError < StandardError; end
+
+class Fasta < Filesys
+ # Method to get the next FASTA entry form an ios and return this
+ # as a Seq object. If no entry is found or eof then nil is returned.
+ def get_entry
+ block = @io.gets($/ + '>')
+ return nil if block.nil?
+
+ block.chomp!($/ + '>')
+
+ (seq_name, seq) = block.split($/, 2)
+
+ raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
+
+ entry = Seq.new
+ entry.type = @type.nil? ? nil : @type.downcase
+ entry.seq = seq.gsub(/\s/, '')
+ entry.seq_name = seq_name.sub(/^>/, '').rstrip
+
+ raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
+ raise FastaError, "Bad FASTA format" if entry.seq.empty?
+
+ entry
+ end
+
+ # TODO - this should be some custom to_s method instead.
+ def puts(record)
+ if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ @io.print ">#{record[:SEQ_NAME]}\n"
+ @io.print "#{record[:SEQ]}\n"
+ end
+ end
+end
+
+
+__END__
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/seq'
+require 'maasha/filesys'
+
+# Error class for all exceptions to do with FASTQ.
+class FastqError < StandardError; end
+
+class Fastq < Filesys
+ # Method to get the next FASTQ entry form an ios and return this
+ # as a Seq object. If no entry is found or eof then nil is returned.
+ def get_entry
+ begin
+ seq_name = @io.gets.chomp!
+ seq = @io.gets.chomp!
+ qual_name = @io.gets.chomp!
+ qual = @io.gets.chomp!
+
+ entry = Seq.new
+ entry.type = @type.nil? ? nil : @type.downcase
+ entry.seq = seq
+ entry.seq_name = seq_name[1 .. seq_name.length]
+ entry.qual = qual
+
+ entry
+ rescue
+ nil
+ end
+ end
+
+ # TODO - this should be some custom to_s method instead.
+ def puts(record)
+ if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ @io.print ">#{record[:SEQ_NAME]}\n"
+ @io.print "#{record[:SEQ]}\n"
+ end
+ end
+end
+
+
+__END__
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'zlib'
+
+# Error class for all exceptions to do with Filesys.
+class FilesysError < StandardError; end
+
+class Filesys
+ include Enumerable
+
+ # Class method that returns a path to a unique temporary file.
+ # If no directory is specified reverts to the systems tmp directory.
+ def self.tmpfile(tmp_dir = ENV["TMPDIR"])
+ time = Time.now.to_i
+ user = ENV["USER"]
+ pid = $$
+ path = tmp_dir + [user, time + pid, pid].join("_") + ".tmp"
+ path
+ end
+
+ # Class method allowing open to be used on (zipped) files.
+ # See File.open.
+ def self.open(*args)
+ args = *args
+ file = args.first
+
+ if file == "-"
+ ios = self.new(STDIN)
+ elsif File.pipe? file
+ ios = self.new(File.open(*args))
+ else
+ ios = self.zopen(*args)
+ end
+
+ if block_given?
+ begin
+ yield ios
+ ensure
+ ios.close
+ end
+ else
+ return ios
+ end
+ end
+
+ def initialize(io, type=nil)
+ @io = io
+ @type = type
+ end
+
+ # Method to close ios.
+ def close
+ @io.close
+ end
+
+ # Iterator method for parsing entries.
+ def each
+ while entry = get_entry do
+ yield entry
+ end
+ end
+
+ private
+
+ # Helper method to return an ios to a file that may be zipped in which case
+ # the ios is unzipped on the fly. See File.open.
+ def self.zopen(*args)
+ ios = File.open(*args)
+
+ begin
+ ios = Zlib::GzipReader.new(ios)
+ rescue
+ ios.rewind
+ end
+
+ self.new(ios)
+ end
+end
--- /dev/null
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/seq'
+require 'maasha/filesys'
+
+# Error class for all exceptions to do with Genbank.
+class GenbankError < StandardError; end
+
+class Genbank < Filesys
+ def initialize(io)
+ @io = io
+ @entry = []
+ end
+
+ # Iterator method for parsing Genbank entries.
+ def each(hash_keys = nil, hash_feats = nil, hash_quals = nil)
+ while @entry = get_entry do
+ keys = get_keys(hash_keys)
+ seq = get_seq
+
+ features = GenbankFeatures.new(@entry, hash_feats, hash_quals)
+
+ features.each do |record|
+ keys.each_pair { |key,val| record[key] = val }
+
+ loc = Locator.new(record[:LOCATOR], seq)
+ record[:SEQ] = loc.subseq.seq
+ record[:SEQ_LEN] = loc.subseq.length
+ record[:STRAND] = loc.strand
+ record[:S_BEG] = loc.s_beg
+ record[:S_END] = loc.s_end
+
+ yield record
+ end
+ end
+ end
+
+ private
+
+ # Method to get the next Genbank entry form an ios and return this.
+ def get_entry
+ block = @io.gets("//" + $/)
+ return nil if block.nil?
+
+ block.chomp!("//" + $/ )
+
+ entry = block.split $/
+
+ return nil if entry.empty?
+
+ entry
+ end
+
+ # Method to get the DNA sequence from a Genbank entry and return
+ # this as a Seq object.
+ def get_seq
+ i = @entry.size
+ j = i - 1
+
+ while @entry[j] and @entry[j] !~ /^[A-Z]/
+ j -= 1
+ end
+
+ seq = @entry[j + 1 .. i].join.delete(" 0123456789")
+
+ Seq.new(nil, seq, "dna") if seq
+ end
+
+ # Method to get the base keys from Genbank entry and return these
+ # in a hash.
+ def get_keys(hash_keys)
+ keys = {}
+ i = 0
+ j = 0
+
+ while @entry[i] and @entry[i] !~ /^FEATURES/
+ if @entry[i] =~ /^\s{0,3}([A-Z]{2})/
+ if want_key?(hash_keys, $1)
+ j = i + 1
+
+ key, val = @entry[i].lstrip.split(/\s+/, 2)
+
+ while @entry[j] and @entry[j] !~ /^\s{0,3}[A-Z]/
+ val << @entry[j].lstrip
+ j += 1
+ end
+
+ if keys[key.to_sym]
+ keys[key.to_sym] << ";" + val
+ else
+ keys[key.to_sym] = val
+ end
+ end
+ end
+
+ j > i ? i = j : i += 1
+ end
+
+ keys
+ end
+
+ def want_key?(hash_keys, key)
+ if hash_keys
+ if hash_keys[key.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+end
+
+class GenbankFeatures
+ @@i = 0
+ @@j = 0
+
+ def initialize(entry, hash_feats, hash_quals)
+ @entry = entry
+ @hash_feats = hash_feats
+ @hash_quals = hash_quals
+ end
+
+ def each
+ while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
+ if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
+ if want_feat? $1
+ record = {}
+
+ feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
+
+ @@j = @@i + 1
+
+ while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+ loc << @entry[@@j].lstrip
+ @@j += 1
+ end
+
+ get_quals.each_pair { |k,v|
+ record[k.upcase.to_sym] = v
+ }
+
+ record[:FEATURE] = feat
+ record[:LOCATOR] = loc
+
+ yield record
+ end
+ end
+
+ @@j > @@i ? @@i = @@j : @@i += 1
+ end
+ end
+
+ private
+
+ def get_quals
+ quals = {}
+ k = 0
+
+ while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
+ if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
+ qual = $1
+ val = $2
+
+ if want_qual? qual
+ k = @@j + 1
+
+ while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+ val << @entry[k].lstrip.chomp('"')
+ k += 1
+ end
+
+ if quals[qual]
+ quals[qual] << ";" + val
+ else
+ quals[qual] = val
+ end
+ end
+ end
+
+ k > @@j ? @@j = k : @@j += 1
+ end
+
+ quals
+ end
+
+ def want_feat?(feat)
+ if @hash_feats
+ if @hash_feats[feat.upcase.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+
+ def want_qual?(qual)
+ if @hash_quals
+ if @hash_quals[qual.upcase.to_sym]
+ return true
+ else
+ return false
+ end
+ else
+ return true
+ end
+ end
+end
+
+
+# Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table locators.
+class LocatorError < StandardError; end
+
+class Locator
+ attr_accessor :locator, :seq, :subseq
+
+ def initialize(locator, seq)
+ @locator = locator
+ @seq = seq
+ @subseq = Seq.new(nil, "", "dna")
+ parse_locator(locator)
+ end
+
+ def strand
+ if @locator.match("complement")
+ return "-"
+ else
+ return "+"
+ end
+ end
+
+ def s_beg
+ if @locator =~ /(\d+)/
+ return $1.to_i - 1
+ end
+ end
+
+ def s_end
+ if @locator.reverse =~ /(\d+)/
+ return $1.reverse.to_i - 1
+ end
+ end
+
+ private
+
+ # Method that uses recursion to parse a locator string from a feature
+ # table and fetches the appropriate subsequence. the operators
+ # join(), complement(), and order() are handled.
+ # the locator string is broken into a comma separated lists, and
+ # modified if the parens donnot balance. otherwise the comma separated
+ # list of ranges are stripped from operators, and the subsequence are
+ # fetched and handled according to the operators.
+ # SNP locators are also dealt with (single positions).
+ def parse_locator(locator, join = nil, comp = nil, order = nil)
+ intervals = locator.split(",")
+
+ unless balance_parens?(intervals.first) # locator includes a join/comp/order of several ranges
+ case locator
+ when /^join\((.*)\)$/
+ locator = $1
+ join = true
+ when /^complement\((.*)\)$/
+ locator = $1
+ comp = true
+ when /^order\((.*)\)$/
+ locator = $1
+ order = true
+ end
+
+ parse_locator(locator, join, comp, order)
+ else
+ intervals.each do |interval|
+ case interval
+ when /^join\((.*)\)$/
+ locator = $1
+ join = true
+ parse_locator(locator, join, comp, order)
+ when /^complement\((.*)\)$/
+ locator = $1
+ comp = true
+ parse_locator(locator, join, comp, order)
+ when /^order\((.*)\)$/
+ locator = $1
+ order = true
+ parse_locator(locator, join, comp, order)
+ when /^[<>]?(\d+)[^\d]+(\d+)$/
+ int_beg = $1.to_i - 1
+ int_end = $2.to_i - 1
+
+ newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
+
+ unless newseq.seq.nil?
+ newseq.revcomp if comp
+
+ @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+ end
+ when /^(\d+)$/
+ pos = $1.to_i - 1
+
+ newseq = Seq.new(nil, @seq.seq[pos], "dna")
+
+ unless newseq.seq.nil?
+ newseq.revcomp if comp
+
+ @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
+ end
+ else
+ $stderr.puts "WARNING: Could not match locator -> #{locator}";
+ @subseq.seq << ""
+ end
+ end
+ end
+
+ return @subseq
+ end
+
+ def balance_parens?(locator)
+ parens = 0
+
+ locator.each_char do |char|
+ case char
+ when '(' then parens += 1
+ when ')' then parens -= 1
+ end
+ end
+
+ if parens == 0
+ return true
+ else
+ return false
+ end
+ end
+end
+
+
+__END__
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/filesys'
+require 'open3'
+
+# Module containing code to locate nucleotide patterns in sequences allowing for
+# ambiguity codes and a given maximum mismatches, insertions, and deletions. The
+# pattern match engine is based on scan_for_matches.
+module Patscan
+ # ------------------------------------------------------------------------------
+ # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]])
+ # -> Array
+ # str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]]) { |match|
+ # block
+ # }
+ # -> Match
+ #
+ # ------------------------------------------------------------------------------
+ # Method to iterate through a sequence to locate pattern matches starting
+ # allowing for a maximum number of mismatches, insertions, and deletions.
+ # Matches found in block context return the Match object. Otherwise matches are
+ # returned in an Array.
+ def scan(pattern, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
+ @pattern = pattern + "[#{max_mismatches},#{max_insertions},#{max_deletions}]"
+ matches = []
+
+ pattern_file = Filesys.tmpfile
+
+ File.open(pattern_file, mode = 'w') do |ios|
+ ios.puts @pattern
+ end
+
+ cmd = "scan_for_matches #{pattern_file}"
+
+ Open3.popen3(cmd) do |stdin, stdout, stderr|
+ #raise SeqError, "scan_for_matches failed: #{stderr.gets}" unless stderr.empty?
+
+ stdin << ">dummy\n#{self.seq}\n"
+
+ stdin.close
+
+ while block = stdout.gets($/ + ">")
+ if block =~ />dummy:\[(\d+),(\d+)\]\n(.+)/
+ start = $1.to_i
+ stop = $2.to_i
+ match = $3.delete(" ")
+ length = stop - start
+
+ if block_given?
+ yield Match.new(start, length, match)
+ else
+ matches << Match.new(start, length, match)
+ end
+ end
+ end
+ end
+
+ matches unless block_given?
+ end
+
+ class Match
+ attr_reader :pos, :length, :match
+
+ def initialize(pos, length, match)
+ @pos = pos
+ @length = length
+ @match = match
+ end
+ end
+end
+
+__END__
+
+
+# Eeeeiiiii - this one is slower than scan_for_matches!
+
+
+# Module containing code to locate nucleotide patterns in sequences allowing for
+# ambiguity codes and a given maximum edit distance. Pattern match engine is based
+# on nrgrep.
+module Patscan
+ # ------------------------------------------------------------------------------
+ # str.scan(pattern[, max_edit_distance])
+ # -> Array
+ # str.scan(pattern[, max_edit_distance]) { |match|
+ # block
+ # }
+ # -> Match
+ #
+ # ------------------------------------------------------------------------------
+ # Method to iterate through a sequence to locate pattern matches starting
+ # from a given position and allowing for a maximum edit distance.
+ # Matches found in block context return the Match object. Otherwise matches are
+ # returned in an Array.
+ def scan(pattern, edit_distance = 0)
+ @pattern = pattern.upcase
+ matches = []
+
+ pattern_disambiguate
+
+ cmd = "nrgrep_coords"
+ cmd << " -i"
+ cmd << " -k #{edit_distance}s" if edit_distance > 0
+ cmd << " #{@pattern}"
+
+ Open3.popen3(cmd) do |stdin, stdout, stderr|
+ stdin << self.seq
+
+ stdin.close
+
+ stdout.each_line do |line|
+ if line =~ /\[(\d+), (\d+)\]: (.+)/
+ start = $1.to_i
+ stop = $2.to_i
+ match = $3
+ length = stop - start
+
+ if block_given?
+ yield Match.new(start, length, match)
+ else
+ matches << Match.new(start, length, match)
+ end
+ end
+ end
+ end
+
+ matches unless block_given?
+ end
+
+ private
+
+ def pattern_disambiguate
+ case self.type
+ when 'protein'
+ @pattern.gsub!('J', '[IFVLWMAGCY]')
+ @pattern.gsub!('O', '[TSHEDQNKR]')
+ @pattern.gsub!('B', '[DN]')
+ @pattern.gsub!('Z', '[EQ]')
+ @pattern.gsub!('X', '.')
+ when 'dna'
+ @pattern.gsub!('R', '[AG]')
+ @pattern.gsub!('Y', '[CT]')
+ @pattern.gsub!('S', '[GC]')
+ @pattern.gsub!('W', '[AT]')
+ @pattern.gsub!('M', '[AC]')
+ @pattern.gsub!('K', '[GT]')
+ @pattern.gsub!('V', '[ACG]')
+ @pattern.gsub!('H', '[ACT]')
+ @pattern.gsub!('D', '[AGT]')
+ @pattern.gsub!('B', '[CGT]')
+ @pattern.gsub!('N', '.')
+ when 'rna'
+ else
+ raise SeqError "unknown sequence type: #{self.type}"
+ end
+ end
+
+ class Match
+ attr_reader :pos, :length, :match
+
+ def initialize(pos, length, match)
+ @pos = pos
+ @length = length
+ @match = match
+ end
+ end
+end
+
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# IUPAC nucleotide pair ambiguity equivalents are saved in an
+# array of bit fields.
+
+BIT_A = 1 << 0
+BIT_T = 1 << 1
+BIT_C = 1 << 2
+BIT_G = 1 << 3
+
+EQUAL = Array.new(256, 0)
+EQUAL['A'.ord] = BIT_A
+EQUAL['a'.ord] = BIT_A
+EQUAL['T'.ord] = BIT_T
+EQUAL['t'.ord] = BIT_T
+EQUAL['U'.ord] = BIT_T
+EQUAL['u'.ord] = BIT_T
+EQUAL['C'.ord] = BIT_C
+EQUAL['c'.ord] = BIT_C
+EQUAL['G'.ord] = BIT_G
+EQUAL['g'.ord] = BIT_G
+EQUAL['M'.ord] = (BIT_A|BIT_C)
+EQUAL['m'.ord] = (BIT_A|BIT_C)
+EQUAL['R'.ord] = (BIT_A|BIT_G)
+EQUAL['r'.ord] = (BIT_A|BIT_G)
+EQUAL['W'.ord] = (BIT_A|BIT_T)
+EQUAL['w'.ord] = (BIT_A|BIT_T)
+EQUAL['S'.ord] = (BIT_C|BIT_G)
+EQUAL['s'.ord] = (BIT_C|BIT_G)
+EQUAL['Y'.ord] = (BIT_C|BIT_T)
+EQUAL['y'.ord] = (BIT_C|BIT_T)
+EQUAL['K'.ord] = (BIT_G|BIT_T)
+EQUAL['k'.ord] = (BIT_G|BIT_T)
+EQUAL['B'.ord] = (BIT_C|BIT_G|BIT_T)
+EQUAL['b'.ord] = (BIT_C|BIT_G|BIT_T)
+EQUAL['D'.ord] = (BIT_A|BIT_G|BIT_T)
+EQUAL['d'.ord] = (BIT_A|BIT_G|BIT_T)
+EQUAL['H'.ord] = (BIT_A|BIT_C|BIT_T)
+EQUAL['h'.ord] = (BIT_A|BIT_C|BIT_T)
+EQUAL['V'.ord] = (BIT_A|BIT_C|BIT_G)
+EQUAL['v'.ord] = (BIT_A|BIT_C|BIT_G)
+EQUAL['N'.ord] = (BIT_A|BIT_C|BIT_G|BIT_T)
+EQUAL['n'.ord] = (BIT_A|BIT_C|BIT_G|BIT_T)
+
+# Module containing code to locate nucleotide patterns in sequences allowing for
+# ambiguity codes and a given maximum edit distance.
+# Insertions are nucleotides found in the pattern but not in the sequence.
+# Deletions are nucleotides found in the sequence but not in the pattern.
+#
+# Inspired by the paper by Bruno Woltzenlogel Paleo (page 197):
+# http://www.logic.at/people/bruno/Papers/2007-GATE-ESSLLI.pdf
+module PatternMatcher
+ # ------------------------------------------------------------------------------
+ # str.match(pattern[, pos[, max_edit_distance]])
+ # -> Match or nil
+ #
+ # ------------------------------------------------------------------------------
+ # Method to locate the next pattern match starting from a given position. A match
+ # is allowed to contain a given maximum edit distance. If a match is located a
+ # Match object will be returned otherwise nil.
+ def match(pattern, pos = 0, max_edit_distance = 0)
+ @pattern = pattern
+ @pos = pos
+ @max_edit_distance = max_edit_distance
+ @vector = vector_init
+
+ while @pos < @seq.length
+ vector_update
+
+ return match_new if match_found?
+
+ @pos += 1
+ end
+ end
+
+ # ------------------------------------------------------------------------------
+ # str.scan(pattern[, pos[, max_edit_distance]])
+ # -> Array
+ # str.scan(pattern[, pos[, max_edit_distance]]) { |match|
+ # block
+ # }
+ # -> Match
+ #
+ # ------------------------------------------------------------------------------
+ # Method to iterate through a sequence to locate pattern matches starting
+ # from a given position and allowing for a maximum edit distance.
+ # Matches found in block context return the Match object. Otherwise matches are
+ # returned in an Array.
+ def scan(pattern, pos = 0, max_edit_distance = 0)
+ matches = []
+
+ while match = match(pattern, pos, max_edit_distance)
+ if block_given?
+ yield match
+ else
+ matches << match
+ end
+
+ pos = match.pos + 1
+ end
+
+ return matches unless block_given?
+ end
+
+ private
+
+ # Method to initailize the score vector and return this.
+ def vector_init
+ vector = []
+
+ (0 ... @pattern.length + 1).each do |i|
+ vector[i] = Score.new(matches = 0, mismatches = 0, insertions = i)
+ end
+
+ vector
+ end
+
+ # Method to update the score vector.
+ def vector_update
+ score_diag = @vector[0]
+ score_up = Score.new # insertion
+ score_left = @vector[1] # deletion
+
+ (0 ... @pattern.length).each do |i|
+ if match?(@seq[@pos], @pattern[i])
+ new_score = score_diag.dup
+ new_score.matches += 1
+ else
+ if deletion?(score_diag, score_up, score_left)
+ new_score = score_left.dup
+ new_score.deletions += 1
+ elsif mismatch?(score_diag, score_up, score_left)
+ new_score = score_diag.dup
+ new_score.mismatches += 1
+ elsif insertion?(score_diag, score_up, score_left)
+ new_score = score_up.dup
+ new_score.insertions += 1
+ end
+ end
+
+ score_diag = @vector[i + 1]
+ score_up = new_score
+ score_left = @vector[i + 2]
+
+ @vector[i + 1] = new_score
+ end
+ end
+
+ # Method to determine if a match occurred.
+ def match?(char1, char2)
+ (EQUAL[char1.ord] & EQUAL[char2.ord]) != 0
+ end
+
+ # Method to determine if a mismatch occured.
+ def mismatch?(score_diag, score_up, score_left)
+ if score_diag.edit_distance <= score_up.edit_distance and
+ score_diag.edit_distance <= score_left.edit_distance
+ true
+ end
+ end
+
+ # Method to determine if an insertion occured.
+ def insertion?(score_diag, score_up, score_left)
+ if score_up.edit_distance <= score_diag.edit_distance and
+ score_up.edit_distance <= score_left.edit_distance
+ true
+ end
+ end
+
+ # Method to determine if a deletion occured.
+ def deletion?(score_diag, score_up, score_left)
+ if score_left.edit_distance <= score_diag.edit_distance and
+ score_left.edit_distance <= score_up.edit_distance
+ true
+ end
+ end
+
+ # Method to print the score vector.
+ def vector_print
+ @vector.each do |s|
+ puts s
+ end
+
+ puts
+ end
+
+ # Method that returns a Match object initialized with
+ # information from the score vector.
+ def match_new
+ matches = @vector.last.matches
+ mismatches = @vector.last.mismatches
+ insertions = @vector.last.insertions
+ deletions = @vector.last.deletions
+ length = @pattern.length - insertions + deletions
+ pos = @pos - length + 1
+ match = @seq[pos ... pos + length]
+
+ Match.new(pos, match, matches, mismatches, insertions, deletions, length)
+ end
+
+ # Method that determines if a match was found by analyzing the score vector.
+ def match_found?
+ if @vector.last.edit_distance <= @max_edit_distance
+ true
+ end
+ end
+
+ # Class to instantiate Score objects that holds score information.
+ class Score
+ attr_accessor :matches, :mismatches, :insertions, :deletions
+
+ def initialize(matches = 0, mismatches = 0, insertions = 0, deletions = 0)
+ @matches = matches
+ @mismatches = mismatches
+ @insertions = insertions
+ @deletions = deletions
+ end
+
+ # Method to calculate and return the edit distance.
+ def edit_distance
+ self.mismatches + self.insertions + self.deletions
+ end
+
+ private
+
+ def to_s
+ "(#{[self.matches, self.mismatches, self.insertions, self.deletions].join(',')})"
+ end
+ end
+
+ # Class for creating Match objects which contain the description of a
+ # match between a nucleotide sequence and a pattern.
+ class Match
+ attr_reader :pos, :match, :matches, :mismatches, :insertions, :deletions, :edit_distance, :length
+
+ def initialize(pos, match, matches, mismatches, insertions, deletions, length)
+ @pos = pos
+ @match = match
+ @matches = matches
+ @mismatches = mismatches
+ @insertions = insertions
+ @deletions = deletions
+ @edit_distance = mismatches + insertions + deletions
+ @length = length
+ end
+ end
+end
--- /dev/null
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/genbank'
+
+# Class for running the Prodigal gene finder.
+# http://prodigal.ornl.gov/
+class Prodigal
+ include Enumerable
+
+ # Method to initialize a Prodigal object
+ # given a temporary infile, outfile and options hash.
+ def initialize(infile, outfile, options)
+ @infile = infile
+ @outfile = outfile
+ @options = options
+ end
+
+ # Method to run Prodigal.
+ def run
+ commands = []
+ commands << "prodigal"
+ commands << "-c" if @options[:full]
+ commands << "-p #{@options[:procedure]}"
+ commands << "-i #{@infile}"
+ commands << "-o #{@outfile}"
+
+ execute(commands, @options[:verbose])
+ end
+
+ # Method for iterating over the Prodigal results,
+ # which are in GenBank format.
+ def each
+ Genbank.open(@outfile, mode='r') do |gb|
+ gb.each do |entry|
+ yield entry
+ end
+ end
+ end
+
+ # Method that returns the sum of the predicted gene lengths.
+ def coverage
+ coverage = 0
+
+ self.each do |gb|
+ coverage += gb[:S_END] - gb[:S_BEG]
+ end
+
+ coverage
+ end
+
+ private
+
+ # Method to execute commands on the command line.
+ # TODO this wants to be in a module on its own.
+ def execute(commands, verbose = false)
+ commands.unshift "nice -n 19"
+ commands.push "> /dev/null 2>&1" unless verbose
+
+ command = commands.join(" ")
+
+ begin
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+ rescue
+ $stderr.puts "Command failed: #{command}"
+ end
+ end
+end
+
+
+__END__
--- /dev/null
+# Copyright (C) 2007-2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/digest'
+require 'maasha/patternmatcher'
+#require 'maasha/patscan'
+
+# Residue alphabets
+DNA = %w[a t c g]
+RNA = %w[a u c g]
+PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
+INDELS = %w[. - _ ~]
+
+# Quality scores bases
+SCORE_PHRED = 33
+SCORE_ILLUMINA = 64
+
+# Error class for all exceptions to do with Seq.
+class SeqError < StandardError; end
+
+class Seq
+ #include Patscan
+ include PatternMatcher
+
+ attr_accessor :seq_name, :seq, :type, :qual
+
+ # Method that generates all possible oligos of a specifed length and type.
+ def self.generate_oligos(length, type)
+ raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
+
+ case type.downcase
+ when /dna/ then alph = DNA
+ when /rna/ then alph = RNA
+ when /protein/ then alph = PROTEIN
+ else
+ raise SeqError, "Unknown sequence type: #{type}"
+ end
+
+ oligos = [""]
+
+ (1 .. length).each do
+ list = []
+
+ oligos.each do |oligo|
+ alph.each do |char|
+ list << oligo + char
+ end
+ end
+
+ oligos = list
+ end
+
+ oligos
+ end
+
+ # Initialize a sequence object with the following arguments:
+ # - seq_name: Name of the sequence.
+ # - seq: The sequence.
+ # - type: The sequence type - DNA, RNA, or protein
+ # - qual: An Illumina type quality scores string.
+ def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
+ @seq_name = seq_name
+ @seq = seq
+ @type = type
+ @qual = qual
+ end
+
+ # Returns the length of a sequence.
+ def length
+ self.seq.nil? ? 0 : self.seq.length
+ end
+
+ alias :len :length
+
+ # Return the number indels in a sequence.
+ def indels
+ regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
+ self.seq.scan(regex).size
+ end
+
+ # Method that returns true is a given sequence type is DNA.
+ def is_dna?
+ self.type == 'dna'
+ end
+
+ # Method that returns true is a given sequence type is RNA.
+ def is_rna?
+ self.type == 'rna'
+ end
+
+ # Method that returns true is a given sequence type is protein.
+ def is_protein?
+ self.type == 'protein'
+ end
+
+ # Method to transcribe DNA to RNA.
+ def to_rna
+ raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
+ raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
+ self.type = 'rna'
+ self.seq.tr!('Tt','Uu')
+ end
+
+ # Method to reverse-transcribe RNA to DNA.
+ def to_dna
+ raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
+ raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
+
+ self.type = 'dna'
+ self.seq.tr!('Uu','Tt')
+ end
+
+ # Method that given a Seq entry returns a Biopieces record (a hash).
+ def to_bp
+ raise SeqError, "Missing seq_name" if self.seq_name.nil?
+ raise SeqError, "Missing seq" if self.seq.nil?
+
+ record = {}
+ record[:SEQ_NAME] = self.seq_name
+ record[:SEQ] = self.seq
+ record[:SEQ_LEN] = self.length
+ record[:SCORES] = self.qual if self.qual
+ record
+ end
+
+ # Method that given a Seq entry returns a FASTA entry (a string).
+ def to_fasta(wrap = nil)
+ raise SeqError, "Missing seq_name" if self.seq_name.nil?
+ raise SeqError, "Missing seq" if self.seq.nil?
+
+ seq_name = self.seq_name
+ seq = self.seq
+
+ unless wrap.nil?
+ seq.gsub!(/(.{#{wrap}})/) do |match|
+ match << "\n"
+ end
+
+ seq.chomp!
+ end
+
+ ">#{seq_name}\n#{seq}\n"
+ end
+
+ # Method that generates a unique key for a
+ # DNA sequence and return this key as a Fixnum.
+ def to_key
+ key = 0
+
+ self.seq.upcase.each_char do |char|
+ key <<= 2
+
+ case char
+ when 'A' then key |= 0
+ when 'C' then key |= 1
+ when 'G' then key |= 2
+ when 'T' then key |= 3
+ else raise SeqError, "Bad residue: #{char}"
+ end
+ end
+
+ key
+ end
+
+ # Method to reverse complement sequence.
+ def reverse_complement
+ self.reverse
+ self.complement
+ end
+
+ alias :revcomp :reverse_complement
+
+ # Method to reverse the sequence.
+ def reverse
+ self.seq.reverse!
+ end
+
+ # Method that complements sequence including ambiguity codes.
+ def complement
+ raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
+
+ if self.is_dna?
+ self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
+ elsif self.is_rna?
+ self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
+ else
+ raise SeqError, "Cannot complement sequence type: #{self.type}"
+ end
+ end
+
+ # Method that generates a random sequence of a given length and type.
+ def generate(length, type)
+ raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
+
+ case type.downcase
+ when "dna"
+ alph = DNA
+ when "rna"
+ alph = RNA
+ when "protein"
+ alph = PROTEIN
+ else
+ raise SeqError, "Unknown sequence type: #{type}"
+ end
+
+ seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
+ self.seq = seq_new
+ self.type = type.downcase
+ seq_new
+ end
+
+ # Method that returns a subsequence of from a given start position
+ # and of a given length.
+ def subseq(start, length = self.length - start)
+ raise SeqError, "subsequence start: #{start} < 0" if start < 0
+ raise SeqError, "subsequence length: #{length} < 1" if length <= 0
+ raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+
+ stop = start + length - 1
+
+ seq = self.seq[start .. stop]
+ qual = self.qual[start .. stop] unless self.qual.nil?
+
+ Seq.new(self.seq_name, seq, self.type, qual)
+ end
+
+ # Method that replaces a sequence with a subsequence from a given start position
+ # and of a given length.
+ def subseq!(start, length = self.length - start)
+ raise SeqError, "subsequence start: #{start} < 0" if start < 0
+ raise SeqError, "subsequence length: #{length} < 1" if length <= 0
+ raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+
+ stop = start + length - 1
+
+ self.seq = self.seq[start .. stop]
+ self.qual = self.qual[start .. stop] unless self.qual.nil?
+ end
+
+ # Method that returns a subsequence of a given length
+ # beginning at a random position.
+ def subseq_rand(length)
+ if self.length - length + 1 == 0
+ start = 0
+ else
+ start = rand(self.length - length + 1)
+ end
+
+ self.subseq(start, length)
+ end
+
+ # Method that returns the residue compositions of a sequence in
+ # a hash where the key is the residue and the value is the residue
+ # count.
+ def composition
+ comp = Hash.new(0);
+
+ self.seq.upcase.each_char do |char|
+ comp[char] += 1
+ end
+
+ comp
+ end
+
+ # Method that returns the length of the longest homopolymeric stretch
+ # found in a sequence.
+ def homopol_max(min = 1)
+ return 0 if self.seq.nil? or self.seq.empty?
+
+ found = false
+
+ self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
+ found = true
+ min = match.size > min ? match.size : min
+ end
+
+ return 0 unless found
+
+ min
+ end
+
+ # Method that returns the percentage of hard masked residues
+ # or N's in a sequence.
+ def hard_mask
+ ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
+ end
+
+ # Method that returns the percentage of soft masked residues
+ # or lower cased residues in a sequence.
+ def soft_mask
+ ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
+ end
+
+ # Method to convert the quality scores from a specified base
+ # to another base.
+ def convert_phred2illumina!
+ self.qual.gsub!(/./) do |score|
+ score_phred = score.ord - SCORE_PHRED
+ raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
+ score_illumina = score_phred + SCORE_ILLUMINA
+ score = score_illumina.chr
+ end
+ end
+
+ # Method to convert the quality scores from Solexa odd/ratio to
+ # Illumina format.
+ def convert_solexa2illumina!
+ self.qual.gsub!(/./) do |score|
+ score = solexa_char2illumina_char(score)
+ end
+ end
+
+ private
+
+ # Method to convert a Solexa score (odd ratio) to
+ # a phred (probability) integer score.
+ def solexa2phred(score)
+ (10.0 * Math.log(10.0 ** (score / 10.0) + 1.0, 10)).to_i
+ end
+
+ # Method to convert a Solexa score encoded using base
+ # 64 ASCII to a Phred score encoded using base 64 ASCII.
+ def solexa_char2illumina_char(char)
+ score_solexa = char.ord - 64
+ score_phred = solexa2phred(score_solexa)
+ (score_phred + 64).chr
+ end
+end
+
+__END__
--- /dev/null
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/base36'
+
+# Error class for all exceptions to do with SFF.
+class SFFError < StandardError; end
+
+BIT_SHIFT = 12
+BIT_MASK = (1 << BIT_SHIFT) - 1
+
+# Class containing methods to parse SFF files:
+# http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff
+class SFF
+ include Enumerable
+
+ @@count = 0
+
+ # Class method for opening SFF files.
+ def self.open(*args)
+ ios = File.open(*args)
+
+ if block_given?
+ begin
+ yield self.new(ios)
+ ensure
+ ios.close
+ end
+ else
+ return self.new(ios)
+ end
+ end
+
+ # Method to initialize an SFF object along with
+ # instance variables pertaining to the SFF header
+ # section.
+ def initialize(io)
+ @io = io
+ @magic_number = 0
+ @version = ""
+ @index_offset = 0
+ @index_length = 0
+ @number_of_reads = 0
+ @header_length = 0
+ @key_length = 0
+ @number_of_flows_per_read = 0
+ @flowgram_format_code = 0
+ @flow_chars = ""
+ @key_sequence = ""
+ @eight_byte_padding = 0
+
+ header_parse
+ end
+
+ # Method to close ios.
+ def close
+ @io.close
+ end
+
+ # Method to iterate over each SFF entry.
+ def each
+ while (read = read_parse) do
+ yield read
+ end
+
+ self # conventionally
+ end
+
+ private
+
+ # Method to parse the SFF file's header section
+ # and load the information into the instance variables.
+ def header_parse
+ template = "NC4N2NNnnnC"
+ bits_in_uint = 32
+
+ data = @io.read(31).unpack(template)
+
+ @magic_number = data[0]
+ @version = data[1 .. 4].join ""
+ @index_offset = (data[5] << bits_in_uint) | data[6]
+ @index_length = data[7]
+ @number_of_reads = data[8]
+ @header_length = data[9]
+ @key_length = data[10]
+ @number_of_flows_per_read = data[11]
+ @flowgram_format_code = data[12]
+ @flow_chars = @io.read(@number_of_flows_per_read).unpack("A*").join ""
+ @key_sequence = @io.read(@key_length).unpack("A*").join ""
+
+ fast_forward
+
+ check_magic_number
+ check_version
+ check_header_length
+ end
+
+ # Method that reads the eight_byte_padding field found at the end of the
+ # data section and fast forwards, i.e. move the file read pointer,
+ # so that the length of the section is divisible by 8.
+ def fast_forward
+ eight_byte_padding = 8 - (@io.pos % 8)
+
+ @io.read(eight_byte_padding) unless eight_byte_padding == 8
+ end
+
+ # Method to parse a read section of an SFF file.
+ def read_parse
+ return nil if @number_of_reads == @@count
+
+ template = "nnNnnnn"
+
+ read = Read.new()
+
+ data = @io.read(16).unpack(template)
+
+ read.read_header_length = data[0]
+ read.name_length = data[1]
+ read.number_of_bases = data[2]
+ read.clip_qual_left = data[3]
+ read.clip_qual_right = data[4]
+ read.clip_adapter_left = data[5]
+ read.clip_adaptor_right = data[6]
+ read.name = @io.read(read.name_length).unpack("A*").join ""
+
+ fast_forward
+
+ @io.read(2 * @number_of_flows_per_read) # skip through flowgram_values
+ @io.read(read.number_of_bases) # skip through flow_index_per_base
+
+ # NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.
+ # read.flowgram_values = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }
+ # flow_index_per_base = @io.read(read.number_of_bases).unpack("C*")
+ # (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }
+ # read.flow_index_per_base = flow_index_per_base
+
+ read.bases = @io.read(read.number_of_bases).unpack("A*").join ""
+ read.quality_scores = @io.read(read.number_of_bases).unpack("C*")
+
+ fast_forward
+
+ @@count += 1
+
+ read
+ end
+
+ # Method to check the magic number of an SFF file.
+ # Raises an error if the magic number don't match.
+ def check_magic_number
+ raise SFFError, "Badly formatted SFF file." unless @magic_number == 779314790
+ end
+
+ # Method to check the version number of an SFF file.
+ # Raises an error if the version don't match.
+ def check_version
+ raise SFFError, "Wrong version: #{@version}" unless @version.to_i == 1
+ end
+
+ # Method to check the header length of an SFF file.
+ # Raises an error if the header length don't match
+ # the file position after reading the header section.
+ def check_header_length
+ raise SFFError, "Bad header length: #{header_length}" unless @io.pos == @header_length
+ end
+end
+
+# Class containing data accessor methods for an SFF entry and methods
+# for manipulating this entry.
+class Read
+ attr_accessor :read_header_length, :name_length, :number_of_bases,
+ :clip_qual_left, :clip_qual_right, :clip_adapter_left, :clip_adaptor_right,
+ :name, :flowgram_values, :flow_index_per_base, :bases, :quality_scores,
+ :x_pos, :y_pos
+
+ # Method that converts a Read object's data to a Biopiece record (a hash).
+ def to_bp
+ coordinates_get
+
+ hash = {}
+
+ hash[:SEQ_NAME] = self.name
+ hash[:SEQ] = self.bases
+ hash[:SEQ_LEN] = self.bases.length
+ hash[:CLIP_QUAL_LEFT] = self.clip_qual_left - 1
+ hash[:CLIP_QUAL_RIGHT] = self.clip_qual_right - 1
+ hash[:CLIP_ADAPTOR_LEFT] = self.clip_adapter_left - 1
+ hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
+ hash[:SCORES] = self.quality_scores.map { |i| (i += 64).chr }.join ""
+ hash[:X_POS] = self.x_pos
+ hash[:Y_POS] = self.y_pos
+
+ hash
+ end
+
+ # Method that soft masks the sequence (i.e. lowercases sequence) according to
+ # clip_qual_left and clip_qual_right information.
+ def mask
+ left = self.bases[0 ... self.clip_qual_left - 1].downcase
+ middle = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
+ right = self.bases[self.clip_qual_right ... self.bases.length].downcase
+
+ self.bases = left + middle + right
+ end
+
+ # Method that clips sequence (i.e. trims) according to
+ # clip_qual_left and clip_qual_right information.
+ def clip
+ self.bases = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
+ self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
+ end
+
+ private
+
+ # Method that extracts the X/Y coordinates from
+ # an SFF read name encoded with base36.
+ def coordinates_get
+ base36 = self.name[-5, 5]
+ num = Base36.decode(base36)
+
+ self.x_pos = num >> BIT_SHIFT
+ self.y_pos = num & BIT_MASK
+ end
+end
+
+__END__
+
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'maasha/base36'
+require 'pp'
+
+class Base36Test < Test::Unit::TestCase
+ def test_Base36_encode_with_non_fixnum_value_raises
+ assert_raise(Base36Error) { Base36.encode("foo") }
+ end
+
+ def test_Base36_encode_returns_correctly
+ assert_equal("AWVHI", Base36.encode(1053908))
+ end
+
+ def test_Base36_decode_with_empty_value_raises
+ assert_raise(Base36Error) { Base36.decode("") }
+ end
+
+ def test_Base36_decode_returns_correctly
+ assert_equal(1053908, Base36.decode("AWVHI"))
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'maasha/biopieces'
+require 'stringio'
+require 'pp'
+
+TYPES = %w[flag string list int uint float file file! files files! dir dir! genome]
+DUMMY_FILE = __FILE__
+SCRIPT_PATH = "write_fasta"
+
+class BiopiecesTest < Test::Unit::TestCase
+
+ def setup
+ @input = StringIO.new
+ @output = StringIO.new
+ @bp = Biopieces.new(true, @input, @output)
+ end
+
+ # >>>>>>>>>>>>>>>>>>>> Testing Options.new <<<<<<<<<<<<<<<<<<<<
+
+ def test_Biopieces_parse_with_all_cast_keys_dont_raise
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_illegal_long_cast_values_raises
+ [nil, true, false, 1, 0, "a"].each do |long|
+ argv = []
+ casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_long_cast_values_dont_raise
+ ["foo", "!!", "0123"].each do |long|
+ argv = []
+ casts = [{:long=>long, :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_short_cast_values_raises
+ [nil, true, false, "foo"].each do |short|
+ argv = []
+ casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_short_cast_values_dont_raise
+ ["!", "1", "a"].each do |short|
+ argv = []
+ casts = [{:long=>"foo", :short=>short, :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_type_cast_values_raises
+ [nil, true, false, "foo", 12, 0].each do |type|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_type_cast_values_dont_raise
+ TYPES.each do |type|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>type, :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_mandatory_cast_values_raises
+ ["yes", 12, 0, nil].each do |mandatory|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_mandatory_cast_values_dont_raise
+ [true, false].each do |mandatory|
+ argv = [ "--foo", "1" ]
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>mandatory, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_default_cast_values_raises
+ [true, false, [], {}].each do |default|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_default_cast_values_dont_raise
+ [nil, 0, 1, -1].each do |default|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>default, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_allowed_cast_values_raises
+ [true, false, {}, [], 0, 0.1].each do |allowed|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_allowed_cast_values_dont_raise
+ ["foo,bar,0",nil].each do |allowed|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>allowed, :disallowed=>nil}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_illegal_disallowed_cast_values_raises
+ [true, false, {}, [], 0, 0.1].each do |disallowed|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_legal_disallowed_cast_values_dont_raise
+ ["foo,bar,0",nil].each do |disallowed|
+ argv = []
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>disallowed}]
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_duplicate_long_cast_values_raises
+ argv = []
+ casts = []
+ casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ casts << {:long=>"foo", :short=>"b", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_duplicate_short_cast_values_raises
+ argv = []
+ casts = []
+ casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ casts << {:long=>"bar", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ assert_raise(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_without_duplicate_long_and_short_cast_values_dont_raise
+ argv = []
+ casts = []
+ casts << {:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ casts << {:long=>"bar", :short=>"b", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+ assert_nothing_raised(CastError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ # >>>>>>>>>>>>>>>>>>>> Testing Options.parse <<<<<<<<<<<<<<<<<<<<
+
+ def test_Biopieces_parse_with_empty_argv_and_missing_wiki_file_raises
+ argv = []
+ casts = []
+ assert_raise(RuntimeError) { @bp.parse(argv,casts, "foo") }
+ end
+
+ def test_Biopieces_parse_with_empty_argv_and_existing_wiki_file_dont_raise
+ argv = []
+ casts = []
+ assert_nothing_raised { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_help_in_argv_and_existing_wiki_output_long_usage
+ argv = ["--help"]
+ assert_nothing_raised { @bp.parse(argv,[],SCRIPT_PATH) }
+ end
+
+# # FIXME This one fails because any argument to a flag is ignored and the flag value is set to true. Should it raise?
+# test "Options.parse with type cast flag with an argument raises
+# casts = [{:long=>"foo", :short=>"f", :type=>"flag", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+# opt_parser = Options.new(casts)
+# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "bar"],SCRIPT_PATH) }
+# end
+
+ def test_Biopieces_parse_with_stream_in_argv_returns_correct_options
+ argv = ["--stream_in", DUMMY_FILE]
+ options = @bp.parse(argv,[],SCRIPT_PATH)
+ assert_equal([DUMMY_FILE], options[:stream_in])
+ end
+
+ def test_Biopieces_parse_with_I_argv_returns_correct_options
+ argv = ["-I", DUMMY_FILE]
+ casts = []
+ options = @bp.parse(argv, casts, SCRIPT_PATH)
+ assert_equal([DUMMY_FILE], options[:stream_in])
+ end
+
+ def test_Biopieces_parse_use_cast_default_value_if_no_argument_given
+ argv = ["-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
+ options = @bp.parse(argv, casts, SCRIPT_PATH)
+ assert_equal(options[:foo], "bar")
+ end
+
+ def test_Biopieces_parse_dont_use_default_value_if_argument_given
+ argv = ["--foo", "bleh", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>"bar", :allowed=>nil, :disallowed=>nil}]
+ options = @bp.parse(argv, casts, SCRIPT_PATH)
+ assert_equal(options[:foo], "bleh".to_sym)
+ end
+
+ def test_Biopieces_parse_with_mandatory_cast_and_no_argument_raises
+ argv = ["-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_mandatory_cast_and_argument_dont_raise
+ argv = ["--foo", "bar", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
+ end
+
+# # This one results in an error: "OptionParser::InvalidArgument: invalid argument: --foo bar"
+# # So it appears that this is tested in OptionParser already.
+# test "Options.parse with type cast int and non-int value raises" do
+# ["bar" ].each do |val| # what about nil, false, true, [], {}, 0.1 ?
+# casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+# opt_parser = Options.new(casts)
+# assert_raise(ArgumentError) { opt_parser.parse(["--foo", "#{val}"],SCRIPT_PATH) }
+# end
+# end
+
+ def test_Biopieces_parse_with_type_cast_int_dont_raise
+ [0,-1,1,327649123746293746374276347824].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"int", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv,casts,SCRIPT_PATH) }
+ end
+ end
+
+ # TODO similar test for uint as "test "Options.parse with type cast int and non-int value raises" do"
+
+ def test_Biopieces_parse_with_type_cast_uint_dont_raise
+ [0,1,327649123746293746374276347824].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"uint", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_file_cast_and_file_dont_exists_raises
+ argv = ["--foo", "bleh", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_file_cast_and_existing_file_dont_raise
+ argv = ["--foo", DUMMY_FILE, "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"file!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_files_cast_and_a_file_dont_exists_raises
+ argv = ["--foo", DUMMY_FILE + ",bleh", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_files_cast_and_files_exists_dont_raise
+ argv = ["--foo", DUMMY_FILE + "," + DUMMY_FILE, "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ # TODO replace the absolute part below the file location with File.dirname(__FILE__)
+ def test_Biopieces_parse_with_glob_argument_expands_correctly
+ flunk("This test is weird")
+ argv = ["--foo", "/Users/maasha/unit_test/foo*,/Users/maasha/unit_test/my_dir/*.fna", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ options = @bp.parse(argv, casts, SCRIPT_PATH)
+ assert_equal(["/Users/maasha/unit_test/foo.fna", "/Users/maasha/unit_test/my_dir/bar.fna"], options[:foo])
+ end
+
+ def test_Biopieces_parse_with_dir_cast_and_dir_dont_exists_raises
+ argv = ["--foo", "bleh", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_dir_cast_and_dir_exists_dont_raise
+ argv = ["--foo", "/", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"dir!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+
+ def test_Biopieces_parse_with_allowed_cast_and_not_allowed_value_raises
+ ["bleh", "2", "3.3"].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
+ assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_allowed_cast_and_allowed_values_dont_raise
+ ["0", "-1", "0.0", "1", "bar"].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>"0,-1,0.0,1,bar", :disallowed=>nil}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_disallowed_cast_and_disallowed_value_raises
+ ["0", "-1", "0.0", "1", "bar"].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
+ assert_raise(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+
+ def test_Biopieces_parse_with_disallowed_cast_and_allowed_values_dont_raise
+ ["bleh", "2", "3.3"].each do |val|
+ argv = ["--foo", "#{val}", "-I", DUMMY_FILE]
+ casts = [{:long=>"foo", :short=>"f", :type=>"string", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0,-1,0.0,1,bar"}]
+ assert_nothing_raised(ArgumentError) { @bp.parse(argv, casts, SCRIPT_PATH) }
+ end
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/bitarray'
+require 'test/unit'
+require 'pp'
+
+class TestBitArray < Test::Unit::TestCase
+ def setup
+ @ba = BitArray.new(10)
+ end
+
+ def test_BitArray_initialize_raises_on_bad_sizes
+ [ -1, 0, 1.1, "a" ].each do |size|
+ assert_raise(BitArrayError) { BitArray.new(size) }
+ end
+ end
+
+ def test_BitArray_initialize_dont_raise_on_ok_sizes
+ [ 1, 10, 1000 ].each do |size|
+ assert_nothing_raised { BitArray.new(size) }
+ end
+ end
+
+ def test_BitArray_size_returns_correctly
+ assert_equal(10, @ba.size)
+ end
+
+ def test_BitArray_to_s_returns_correctly
+ assert_equal("0000000000", @ba.to_s)
+ end
+
+ def test_BitArray_bit_set_with_bad_pos_raises
+ [-1, 10, 1.1].each do |pos|
+ assert_raise(BitArrayError) { @ba.bit_set(pos) }
+ end
+ end
+
+ def test_BitArray_bit_set
+ str = "0000000000"
+
+ (0.upto 9).each do |pos|
+ @ba.bit_set(pos)
+ str[pos] = "1"
+ assert_equal(str, @ba.to_s)
+ end
+ end
+
+ def test_BitArray_bit_set_questionmark_with_bad_pos_raises
+ [-1, 10, 1.1].each do |pos|
+ assert_raise(BitArrayError) { @ba.bit_set?(pos) }
+ end
+ end
+
+ def test_BitArray_bit_set_questionmark
+ (0.upto 9).each do |pos|
+ @ba.bit_set(pos)
+ assert_equal(true, @ba.bit_set?(pos))
+ end
+ end
+
+ def test_BitArray_bits_on_returns_correctly
+ @ba.bit_set(4)
+ @ba.bit_set(0)
+ @ba.bit_set(1)
+ assert_equal(3, @ba.bits_on)
+ end
+
+ def test_BitArray_bits_off_returns_correctly
+ @ba.bit_set(4)
+ assert_equal(9, @ba.bits_off)
+ end
+
+ def test_BitArray_AND_with_uneven_sizes_raises
+ ba = BitArray.new(11)
+ assert_raise(BitArrayError) { @ba & ba }
+ end
+
+ def test_BitArray_AND_returns_correctly
+ ba = BitArray.new(10)
+ @ba.bit_set(4)
+ @ba.bit_set(5)
+ ba.bit_set(5)
+ ba.bit_set(6)
+ assert_equal( "0000010000", (@ba & ba).to_s)
+ end
+
+ def test_BitArray_OR_with_uneven_sizes_raises
+ ba = BitArray.new(11)
+ assert_raise(BitArrayError) { @ba | ba }
+ end
+
+ def test_BitArray_OR_returns_correctly
+ ba = BitArray.new(10)
+ @ba.bit_set(4)
+ @ba.bit_set(5)
+ ba.bit_set(5)
+ ba.bit_set(6)
+ assert_equal( "0000111000", (@ba | ba).to_s)
+ end
+
+ def test_BitArray_XOR_with_uneven_sizes_raises
+ ba = BitArray.new(11)
+ assert_raise(BitArrayError) { @ba ^ ba }
+ end
+
+ def test_BitArray_XOR_returns_correctly
+ ba = BitArray.new(10)
+ @ba.bit_set(4)
+ @ba.bit_set(5)
+ ba.bit_set(5)
+ ba.bit_set(6)
+ assert_equal( "0000101000", (@ba ^ ba).to_s)
+ end
+end
+
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/bits'
+require 'test/unit'
+require 'pp'
+
+class TestBits < Test::Unit::TestCase
+ def test_Bits_hamming_dist_with_uneven_lengths_raises
+ assert_raises(StringError) { String.hamming_dist("ATCG", "ATC") }
+ end
+
+ def test_Bits_hamming_dist_with_even_lengths_dont_raise
+ assert_nothing_raised { String.hamming_dist("ATCG", "ATCG") }
+ end
+
+ def test_Bits_hamming_dist_returns_correctly
+ assert_equal(0, String.hamming_dist("ATCG", "ATCG"))
+ assert_equal(1, String.hamming_dist("ATCX", "ATCG"))
+ assert_equal(2, String.hamming_dist("ATXX", "ATCG"))
+ assert_equal(2, String.hamming_dist("ATcg", "ATCG"))
+ assert_equal(3, String.hamming_dist("AXXX", "ATCG"))
+ assert_equal(4, String.hamming_dist("XXXX", "ATCG"))
+ end
+
+ def test_Bits_AND_with_equal_length_returns_correctly
+ assert_equal("ABCD", "abcd" & "____")
+ end
+
+ def test_Bits_AND_with_unequal_length_returns_correctly
+ assert_equal("JAPH\n", "japh\nJunk" & '_____')
+ assert_equal("JAPH\n", '_____' & "japh\nJunk")
+ end
+
+ def test_Bits_OR_with_equal_length_returns_correctly
+ assert_equal("abcd", "ab " | " cd")
+ end
+
+ def test_Bits_OR_with_unequal_length_returns_correctly
+ assert_equal("japh\n", "JA" | " ph\n")
+ assert_equal("japh\n", " ph\n" | "JA")
+ end
+
+ def test_Bits_XOR_with_equal_length_returns_correctly
+ assert_equal("ABCD", "ab " ^ " cd")
+ end
+
+ def test_Bits_XOR_with_unequal_length_returns_correctly
+ assert_equal("JAPH", "j p \n" ^ " a h")
+ assert_equal("JAPH", " a h" ^ "j p \n")
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/boulder'
+require 'test/unit'
+require 'stringio'
+require 'pp'
+
+class TestBoulder < Test::Unit::TestCase
+ def test_Boulder_each_raises_on_missing_seperator
+ boulder = Boulder.new(StringIO.new("TEST_BAD=testbad\n"))
+ assert_raise(BoulderError) { boulder.each }
+ end
+
+ def test_Boulder_each_raises_on_missing_key_val_seperator
+ boulder = Boulder.new(StringIO.new("TEST_BAD\n=\n"))
+ assert_raise(BoulderError) { boulder.each }
+ end
+
+ def test_Boulder_each_raises_on_missing_value
+ boulder = Boulder.new(StringIO.new("TEST_BAD=\n=\n"))
+ assert_raise(BoulderError) { boulder.each }
+ end
+
+ def test_Boulder_each_raises_on_missing_key
+ boulder = Boulder.new(StringIO.new("=testbad\n=\n"))
+ assert_raise(BoulderError) { boulder.each }
+ end
+
+ def test_Boulder_each_with_one_key_val_pair_returns_correctly
+ boulder = Boulder.new(StringIO.new("TEST0=thisistest0\n=\n"))
+
+ boulder.each do |record|
+ assert_equal({:TEST0=>'thisistest0'},record)
+ end
+ end
+
+ def test_Boulder_each_with_two_key_val_pairs_return_correctly
+ boulder = Boulder.new(StringIO.new("TEST0=thisistest0\nTEST1=thisistest1\n=\n"))
+
+ boulder.each do |record|
+ assert_equal({:TEST0=>'thisistest0', :TEST1=>'thisistest1'},record)
+ end
+ end
+
+ def test_Boulder_to_boulder_returns_correctly
+ boulder = Boulder.new()
+
+ assert_equal("TEST0=thisistest0\n=\n", boulder.to_boulder({:TEST0=>'thisistest0'}))
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'maasha/seq'
+require 'test/unit'
+require 'pp'
+
+class TestDigest < Test::Unit::TestCase
+ def setup
+ @entry = Seq.new
+ end
+
+ def test_Digest_new_raises_on_bad_pattern_residue
+ assert_raise(DigestError) { Digest.new(@entry, "X", 4) }
+ end
+
+ def test_Digest_new_dont_raise_on_ok_pattern_residue
+ assert_nothing_raised { Digest.new(@entry, "AGCUTRYWSMKHDVBNagcutrywsmkhdvbn", 4) }
+ end
+
+ def test_Digest_each
+ @entry.seq = "aaaaTTTTbbbbTTTT"
+ digest = Digest.new(@entry, "TTNT", 1)
+ assert_equal("aaaaT", digest.first.seq)
+ end
+end
+
+
+__END__
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'maasha/fasta'
+require 'stringio'
+require 'pp'
+
+class FastaTest < Test::Unit::TestCase
+ def test_Fasta_get_entry_obtains_the_correct_seq_name
+ fasta = Fasta.new(StringIO.new(">test\nATCG\n"))
+ assert_equal(fasta.get_entry.seq_name, "test")
+ end
+
+ def test_Fasta_get_entry_obtains_the_correct_seq_without_trailing_newlines
+ fasta = Fasta.new(StringIO.new(">test\nATCG"))
+ assert_equal(fasta.get_entry.seq, "ATCG")
+ end
+
+ def test_Fasta_get_entry_obtains_the_correct_seq_with_trailing_newlines
+ fasta = Fasta.new(StringIO.new(">test\nATCG\n\n\n"))
+ assert_equal(fasta.get_entry.seq, "ATCG")
+ end
+
+ def test_Fasta_get_entry_obtains_the_correct_type
+ fasta = Fasta.new(StringIO.new(">test\nATCG\n"), 'DNA')
+ assert_equal(fasta.get_entry.type, "dna")
+ end
+
+ def test_Fasta_get_entry_rstrips_whitespace_from_seq_name
+ fasta = Fasta.new(StringIO.new(">test\n\r\t ATCG\n"))
+ assert_equal(fasta.get_entry.seq_name, "test")
+ end
+
+ def test_Fasta_get_entry_strips_whitespace_from_seq
+ fasta = Fasta.new(StringIO.new(">test\n\r\t AT\n\r\t CG\n\r\t "))
+ assert_equal(fasta.get_entry.seq, "ATCG")
+ end
+
+ def test_Fasta_get_entry_with_two_entries_obtain_correct
+ fasta = Fasta.new(StringIO.new(">test1\n\r\t AT\n\r\t CG\n\r\t \n>test2\n\r\t atcg\n"))
+ assert_equal(fasta.get_entry.seq, "ATCG")
+ assert_equal(fasta.get_entry.seq, "atcg")
+ end
+
+ def test_Fasta_get_entry_without_seq_name_raises
+ fasta = Fasta.new(StringIO.new("ATCG\n"))
+ assert_raise( FastaError ) { fasta.get_entry }
+ end
+
+ def test_Fasta_get_entry_without_seq_raises
+ fasta = Fasta.new(StringIO.new(">test\n\n"))
+ assert_raise( FastaError ) { fasta.get_entry }
+ end
+
+ def test_Fasta_get_entry_with_leading_newline_raises
+ fasta = Fasta.new(StringIO.new("\n>test\nATCG\n"))
+ assert_raise( FastaError ) { fasta.get_entry }
+ end
+
+# FIXME
+# def test_Fasta_get_entry raises on missing > in seq_name
+# fasta = Fasta.new(StringIO.new("test\nATCG\n"))
+# assert_raise( FastaError ) { fasta.get_entry }
+# end
+end
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'maasha/fastq'
+require 'stringio'
+require 'pp'
+
+class FastqTest < Test::Unit::TestCase
+ def setup
+ @io = StringIO.new("@test1\nATCG\n+\nABCD\n@test2\natcg\n+test2\n@ABG\n")
+ @fastq = Fastq.new(@io)
+ end
+
+ def test_Fastq_get_entry_obtains_the_correct_seq_name
+ assert_equal("test1", @fastq.get_entry.seq_name)
+ end
+
+ def test_Fasta_get_entry_obtains_the_correct_type
+ fastq = Fastq.new(@io, 'DNA')
+ assert_equal("dna", fastq.get_entry.type)
+ end
+
+ def test_Fastq_get_entry_with_two_entries_obtain_correct
+ assert_equal("ATCG", @fastq.get_entry.seq)
+ assert_equal("atcg", @fastq.get_entry.seq)
+ end
+
+ def test_Fastq_each_loop_ends_correctly
+ @fastq.each do |entry|
+ end
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/genbank'
+require 'maasha/seq'
+require 'test/unit'
+require 'pp'
+
+class TestGenbank < Test::Unit::TestCase
+ def setup
+ @seq = Seq.new(nil, "tcatgatcaagatctaacagcagaagtacacttctattta", "dna")
+ end
+
+ def test_Locator_with_single_position_returns_correctly
+ loc = Locator.new("10", @seq)
+ assert_equal("a", loc.subseq.seq)
+ end
+
+ def test_Locator_with_single_interval_returns_correctly
+ loc = Locator.new("5..10", @seq)
+ assert_equal("gatca", loc.subseq.seq)
+ end
+
+ def test_Locator_with_multiple_intervals_return_correctly
+ loc = Locator.new("5..10,15..20", @seq)
+ assert_equal("gatcataaca", loc.subseq.seq)
+ end
+
+ def test_Locator_with_join_multiple_intervals_return_correctly
+ loc = Locator.new("join(5..10,15..20)", @seq)
+ assert_equal("gatcataaca", loc.subseq.seq)
+ end
+
+ def test_Locator_with_complement_and_single_interval_return_correctly
+ loc = Locator.new("complement(5..10)", @seq)
+ assert_equal("tgatc", loc.subseq.seq)
+ end
+end
+
+
+__END__
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/seq'
+require 'test/unit'
+require 'pp'
+
+class TestPatternMatcher < Test::Unit::TestCase
+ def setup
+ @p = Seq.new("test", "atcg")
+ end
+
+ def test_PatternMatcher_no_match_returns_nil
+ assert_nil(@p.match("gggg"))
+ end
+
+ def test_PatternMatcher_match_perfect_returns_correctly
+ m = @p.match("atcg")
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(4, m.matches)
+ assert_equal(0, m.mismatches)
+ assert_equal(0, m.insertions)
+ assert_equal(0, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_match_perfect_with_ambiguity_codes_returns_correctly
+ m = @p.match("nnnn")
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(4, m.matches)
+ assert_equal(0, m.mismatches)
+ assert_equal(0, m.insertions)
+ assert_equal(0, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_zero_returns_nil
+ assert_nil(@p.match("aCcg"))
+ end
+
+ def test_PatternMatcher_match_with_one_mismatch_and_edit_dist_one_returns_correctly
+ m = @p.match("aCcg", pos = 0, edit_distance = 1)
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(3, m.matches)
+ assert_equal(1, m.mismatches)
+ assert_equal(0, m.insertions)
+ assert_equal(0, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_match_with_two_mismatch_and_edit_dist_one_returns_nil
+ assert_nil(@p.match("aGcA", pos = 0, edit_distance = 1))
+ end
+
+ def test_PatternMatcher_match_with_one_insertion_and_edit_dist_zero_returns_nil
+ assert_nil(@p.match("atGcg"))
+ end
+
+ def test_PatternMatcher_match_with_one_insertion_and_edit_dist_one_returns_correctly
+ m = @p.match("atGcg", pos = 0, edit_distance = 1)
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(4, m.matches)
+ assert_equal(0, m.mismatches)
+ assert_equal(1, m.insertions)
+ assert_equal(0, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_match_with_two_insertions_and_edit_dist_one_returns_nil
+ assert_nil(@p.match("atGcTg", pos = 0, edit_distance = 1))
+ end
+
+ def test_PatternMatcher_match_with_two_insertions_and_edit_dist_two_returns_correctly
+ m = @p.match("atGcTg", pos = 0, edit_distance = 2)
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(4, m.matches)
+ assert_equal(0, m.mismatches)
+ assert_equal(2, m.insertions)
+ assert_equal(0, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_match_with_one_deletion_and_edit_distance_zero_returns_nil
+ assert_nil(@p.match("acg"))
+ end
+
+ def test_PatternMatcher_match_with_one_deletion_and_edit_distance_one_returns_correctly
+ m = @p.match("acg", pos = 0, edit_distance = 1)
+ assert_equal(0, m.pos)
+ assert_equal("atcg", m.match)
+ assert_equal(3, m.matches)
+ assert_equal(0, m.mismatches)
+ assert_equal(0, m.insertions)
+ assert_equal(1, m.deletions)
+ assert_equal(4, m.length)
+ end
+
+ def test_PatternMatcher_scan_locates_three_patterns_ok
+ p = Seq.new("test", "ataacgagctagctagctagctgactac")
+ assert_equal(3, p.scan("tag").count)
+ end
+
+ def test_PatternMatcher_scan_with_pos_locates_two_patterns_ok
+ p = Seq.new("test", "ataacgagctagctagctagctgactac")
+ assert_equal(2, p.scan("tag", 10).count)
+ end
+end
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'maasha/seq'
+require 'test/unit'
+require 'pp'
+
+class TestSeq < Test::Unit::TestCase
+ def setup
+ @entry = Seq.new
+ end
+
+ # def test_Seq# autoremoves whitespace, newlines, and carriage returns
+ # dna = Seq.new
+ # dna.seq = "A\tT\r\tC\nG "
+ # assert_equal(dna.seq, "ATCG")
+ # end
+
+ def test_Seq_is_dna_with_no_sequence_type_returns_false
+ assert(@entry.is_dna? == false)
+ end
+
+ def test_Seq_is_dna_with_dna_sequence_type_returns_true
+ @entry.type = 'dna'
+ assert(@entry.is_dna? == true)
+ end
+
+ def test_Seq_is_rna_with_no_sequence_type_returns_false
+ assert(@entry.is_rna? == false)
+ end
+
+ def test_Seq_is_rna_with_rna_sequence_type_returns_true
+ @entry.type = 'rna'
+ assert(@entry.is_rna? == true)
+ end
+
+ def test_Seq_is_protein_with_no_sequence_type_returns_false
+ assert(@entry.is_protein? == false)
+ end
+
+ def test_Seq_is_protein_with_protein_sequence_type_returns_true
+ @entry.type = 'protein'
+ assert(@entry.is_protein? == true)
+ end
+
+ def test_Seq_length_is_correct
+ @entry.seq = 'ATCG'
+ assert_equal(4, @entry.length)
+ end
+
+ def test_Seq_indels_is_correct
+ @entry.seq = 'ATCG.-~_'
+ assert_equal(4, @entry.indels)
+ end
+
+ def test_Seq_to_rna_raises_if_no_sequence
+ @entry.type = 'dna'
+ assert_raise(SeqError) { @entry.to_rna }
+ end
+
+ def test_Seq_to_rna_raises_on_bad_type
+ @entry.seq = 'ATCG'
+ @entry.type = 'rna'
+ assert_raise(SeqError) { @entry.to_rna }
+ end
+
+ def test_Seq_to_rna_transcribes_correctly
+ @entry.seq = 'ATCGatcg'
+ @entry.type = 'dna'
+ assert_equal("AUCGaucg", @entry.to_rna)
+ end
+
+ def test_Seq_to_rna_changes_entry_type_to_rna
+ @entry.seq = 'ATCGatcg'
+ @entry.type = 'dna'
+ @entry.to_rna
+ assert_equal("rna", @entry.type)
+ end
+
+ def test_Seq_to_dna_raises_if_no_sequence
+ @entry.type = 'rna'
+ assert_raise(SeqError) { @entry.to_dna }
+ end
+
+ def test_Seq_to_dna_raises_on_bad_type
+ @entry.seq = 'AUCG'
+ @entry.type = 'dna'
+ assert_raise(SeqError) { @entry.to_dna }
+ end
+
+ def test_Seq_to_dna_transcribes_correctly
+ @entry.seq = 'AUCGaucg'
+ @entry.type = 'rna'
+ assert_equal("ATCGatcg", @entry.to_dna)
+ end
+
+ def test_Seq_to_dna_changes_entry_type_to_dna
+ @entry.seq = 'AUCGaucg'
+ @entry.type = 'rna'
+ @entry.to_dna
+ assert_equal("dna", @entry.type)
+ end
+
+ def test_Seq_to_bp_returns_correct_record
+ @entry.seq_name = 'test'
+ @entry.seq = 'ATCG'
+ assert_equal({:SEQ_NAME=>"test", :SEQ=>"ATCG", :SEQ_LEN=>4}, @entry.to_bp)
+ end
+
+ def test_Seq_to_bp_raises_on_missing_seq_name
+ @entry.seq = 'ATCG'
+ assert_raise(SeqError) { @entry.to_bp }
+ end
+
+ def test_Seq_to_bp_raises_on_missing_sequence
+ @entry.seq_name = 'test'
+ assert_raise(SeqError) { @entry.to_bp }
+ end
+
+ def test_Seq_to_fasta_returns_correct_entry
+ @entry.seq_name = 'test'
+ @entry.seq = 'ATCG'
+ assert_equal(">test\nATCG\n", @entry.to_fasta)
+ end
+
+ def test_Seq_to_fasta_wraps_correctly
+ entry = Seq.new("test", "ATCG")
+ assert_equal(">test\nAT\nCG\n", entry.to_fasta(2))
+ end
+
+ def test_Seq_to_key_with_bad_residue_raises
+ entry = Seq.new("test", "AUCG")
+ assert_raise(SeqError) { entry.to_key }
+ end
+
+ def test_Seq_to_key_returns_correctly
+ entry = Seq.new("test", "ATCG")
+ assert_equal(54, entry.to_key)
+ end
+
+ def test_Seq_reverse_returns_correctly
+ @entry.seq = "ATCG"
+ assert_equal("GCTA", @entry.reverse)
+ end
+
+ def test_Seq_complement_raises_if_no_sequence
+ @entry.type = 'dna'
+ assert_raise(SeqError) { @entry.complement }
+ end
+
+ def test_Seq_complement_raises_on_bad_type
+ @entry.seq = 'ATCG'
+ @entry.type = 'protein'
+ assert_raise(SeqError) { @entry.complement }
+ end
+
+ def test_Seq_complement_for_DNA_is_correct
+ @entry.seq = 'ATCGatcg'
+ @entry.type = 'dna'
+ assert_equal("TAGCtagc", @entry.complement)
+ end
+
+ def test_Seq_complement_for_RNA_is_correct
+ @entry.seq = 'AUCGaucg'
+ @entry.type = 'rna'
+ assert_equal("UAGCuagc", @entry.complement)
+ end
+
+ def test_Seq_reverse_complement_for_DNA_is_correct
+ @entry.seq = 'ATCGatcg'
+ @entry.type = 'dna'
+ assert_equal("cgatCGAT", @entry.reverse_complement)
+ end
+
+ def test_Seq_reverse_complement_for_RNA_is_correct
+ @entry.seq = 'AUCGaucg'
+ @entry.type = 'rna'
+ assert_equal("cgauCGAU", @entry.reverse_complement)
+ end
+
+ def test_Seq_generate_with_length_lt_1_raises
+ assert_raise(SeqError) { @entry.generate(-10, "dna") }
+ assert_raise(SeqError) { @entry.generate(0, "dna") }
+ end
+
+ def test_Seq_generate_with_bad_type_raises
+ assert_raise(SeqError) { @entry.generate(10, "foo") }
+ end
+
+ def test_Seq_generate_with_ok_type_dont_raise
+ %w[dna DNA rna RNA protein Protein].each do |type|
+ assert_nothing_raised { @entry.generate(10, type) }
+ end
+ end
+
+ def test_Seq_subseq_with_start_lt_0_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq(-1, 1) }
+ end
+
+ def test_Seq_subseq_with_length_lt_1_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq(0, 0) }
+ end
+
+ def test_Seq_subseq_with_start_plus_length_gt_seq_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq(0, 5) }
+ end
+
+ def test_Seq_subseq_returns_correct_sequence
+ @entry.seq = "ATCG"
+ assert_equal("AT", @entry.subseq(0, 2).seq)
+ assert_equal("CG", @entry.subseq(2, 2).seq)
+ end
+
+ def test_Seq_subseq_without_len_returns_correct_sequence
+ @entry.seq = "ATCG"
+ assert_equal("ATCG", @entry.subseq(0).seq)
+ assert_equal("CG", @entry.subseq(2).seq)
+ end
+
+ def test_Seq_subseq_returns_correct_qual
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ assert_equal("ab", @entry.subseq(0, 2).qual)
+ assert_equal("cd", @entry.subseq(2, 2).qual)
+ end
+
+ def test_Seq_subseq_without_len_returns_correct_qual
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ assert_equal("abcd", @entry.subseq(0).qual)
+ assert_equal("cd", @entry.subseq(2).qual)
+ end
+
+ def test_Seq_subseq_bang_with_start_lt_0_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq!(-1, 1) }
+ end
+
+ def test_Seq_subseq_bang_with_length_lt_1_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq!(0, 0) }
+ end
+
+ def test_Seq_subseq_bang_with_start_plus_length_gt_seq_raises
+ @entry.seq = "ATCG"
+ assert_raise(SeqError) { @entry.subseq!(0, 5) }
+ end
+
+ def test_Seq_subseq_bang_returns_correct_sequence
+ @entry.seq = "ATCG"
+ @entry.subseq!(0, 2)
+ assert_equal("AT", @entry.seq)
+ @entry.seq = "ATCG"
+ @entry.subseq!(2, 2)
+ assert_equal("CG", @entry.seq)
+ end
+
+ def test_Seq_subseq_bang_without_len_returns_correct_sequence
+ @entry.seq = "ATCG"
+ @entry.subseq!(0)
+ assert_equal("ATCG", @entry.seq)
+ @entry.seq = "ATCG"
+ @entry.subseq!(2)
+ assert_equal("CG", @entry.seq)
+ end
+
+ def test_Seq_subseq_bang_with_pos_and_len_returns_correct_qual
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ @entry.subseq!(0, 2)
+ assert_equal("ab", @entry.qual)
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ @entry.subseq!(2, 2)
+ assert_equal("cd", @entry.qual)
+ end
+
+ def test_Seq_subseq_bang_with_pos_returns_correct_qual
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ @entry.subseq!(0)
+ assert_equal("abcd", @entry.qual)
+ @entry.seq = "ATCG"
+ @entry.qual = "abcd"
+ @entry.subseq!(2)
+ assert_equal("cd", @entry.qual)
+ end
+
+ def test_Seq_subseq_rand_returns_correct_sequence
+ @entry.seq = "ATCG"
+ assert_equal("ATCG", @entry.subseq_rand(4).seq)
+ end
+
+ def test_Seq_composition_returns_correctly
+ @entry.seq = "AAAATTTCCG"
+ assert_equal(4, @entry.composition["A"])
+ assert_equal(3, @entry.composition["T"])
+ assert_equal(2, @entry.composition["C"])
+ assert_equal(1, @entry.composition["G"])
+ assert_equal(0, @entry.composition["X"])
+ end
+
+ def test_Seq_homopol_max_returns_0_with_empty_sequence
+ @entry.seq = ""
+ assert_equal(0, @entry.homopol_max)
+ end
+
+ def test_Seq_homopol_max_returns_0_with_nil_sequence
+ @entry.seq = nil
+ assert_equal(0, @entry.homopol_max)
+ end
+
+ def test_Seq_homopol_max_returns_0_when_not_found
+ @entry.seq = "AtTcCcGggGnnNnn"
+ assert_equal(0, @entry.homopol_max(6))
+ end
+
+ def test_Seq_homopol_max_returns_correctly
+ @entry.seq = "AtTcCcGggGnnNnn"
+ assert_equal(5, @entry.homopol_max(3))
+ end
+
+ def test_Seq_hard_mask_returns_correctly
+ @entry.seq = "--AAAANn"
+ assert_equal(33.33, @entry.hard_mask)
+ end
+
+ def test_Seq_soft_mask_returns_correctly
+ @entry.seq = "--AAAa"
+ assert_equal(25.00, @entry.soft_mask)
+ end
+end
+
+
+__END__
projects / biopieces.git / commitdiff
