From 494dc53ebd515b1e3e9b91bbebf43059899ca4ce Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 13 May 2011 19:46:09 +0000 Subject: [PATCH] changed layout of ruby source git-svn-id: http://biopieces.googlecode.com/svn/trunk@1405 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/analyze_assembly | 6 +- bp_bin/analyze_seq | 4 +- bp_bin/assemble_seq_idba | 4 +- bp_bin/assemble_seq_velvet | 4 +- bp_bin/bin_vals | 2 +- bp_bin/calc_N50 | 2 +- bp_bin/clip_adaptor | 2 +- bp_bin/clip_seq | 2 +- bp_bin/digest_seq | 6 +- bp_bin/find_adaptor | 4 +- bp_bin/find_genes | 6 +- bp_bin/find_homopolymers | 4 +- bp_bin/find_mids | 2 +- bp_bin/join_seq | 6 +- bp_bin/kmer_freq | 4 +- bp_bin/length_seq | 2 +- bp_bin/mask_seq | 2 +- bp_bin/pcr_seq | 6 +- bp_bin/plot_scores | 2 +- bp_bin/progress_meter | 2 +- bp_bin/read_fasta | 4 +- bp_bin/read_fastq | 4 +- bp_bin/read_genbank | 4 +- bp_bin/read_sff | 4 +- bp_bin/remove_mids | 2 +- bp_bin/scores_to_dec | 2 +- bp_bin/shred_seq | 4 +- bp_bin/shuffle_records | 2 +- bp_bin/swapcase_seq | 2 +- bp_bin/uclust_seq | 4 +- bp_conf/bashrc | 2 +- code_ruby/Maasha/Rakefile | 6 - code_ruby/Maasha/lib/doc/Base36.html | 316 --- code_ruby/Maasha/lib/doc/Base36Error.html | 200 -- code_ruby/Maasha/lib/doc/Biopieces.html | 562 ----- code_ruby/Maasha/lib/doc/BitArray.html | 869 -------- code_ruby/Maasha/lib/doc/BitArrayError.html | 201 -- code_ruby/Maasha/lib/doc/Boulder.html | 361 ---- code_ruby/Maasha/lib/doc/BoulderError.html | 201 -- code_ruby/Maasha/lib/doc/CastError.html | 200 -- code_ruby/Maasha/lib/doc/Casts.html | 823 -------- code_ruby/Maasha/lib/doc/Digest.html | 416 ---- code_ruby/Maasha/lib/doc/DigestError.html | 200 -- code_ruby/Maasha/lib/doc/Fasta.html | 308 --- code_ruby/Maasha/lib/doc/FastaError.html | 200 -- code_ruby/Maasha/lib/doc/Fastq.html | 306 --- code_ruby/Maasha/lib/doc/FastqError.html | 200 -- code_ruby/Maasha/lib/doc/Filesys.html | 452 ---- code_ruby/Maasha/lib/doc/FilesysError.html | 201 -- code_ruby/Maasha/lib/doc/Genbank.html 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(99%) rename code_ruby/{Maasha/lib => lib/maasha}/patscan.rb (99%) rename code_ruby/{Maasha/lib => lib/maasha}/patternmatcher.rb (100%) rename code_ruby/{Maasha/lib => lib/maasha}/prodigal.rb (99%) rename code_ruby/{Maasha/lib => lib/maasha}/seq.rb (99%) rename code_ruby/{Maasha/lib => lib/maasha}/sff.rb (99%) rename code_ruby/{Maasha/test => test/maasha}/test_base36.rb (98%) rename code_ruby/{Maasha/test => test/maasha}/test_biopieces.rb (99%) rename code_ruby/{Maasha/test => test/maasha}/test_bitarray.rb (99%) rename code_ruby/{Maasha/test => test/maasha}/test_bits.rb (99%) create mode 100755 code_ruby/test/maasha/test_boulder.rb rename code_ruby/{Maasha/test => test/maasha}/test_digest.rb (96%) rename code_ruby/{Maasha/test => test/maasha}/test_fasta.rb (99%) rename code_ruby/{Maasha/test => test/maasha}/test_fastq.rb (98%) rename code_ruby/{Maasha/test => test/maasha}/test_genbank.rb (97%) rename code_ruby/{Maasha/test => test/maasha}/test_patternmatcher.rb (99%) rename code_ruby/{Maasha/test => test/maasha}/test_seq.rb (99%) diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly index a946d2c..bcc727c 100755 --- a/bp_bin/analyze_assembly +++ b/bp_bin/analyze_assembly @@ -29,9 +29,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'fasta' -require 'prodigal' +require 'maasha/biopieces' +require 'maasha/fasta' +require 'maasha/prodigal' require 'pp' casts = [] diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq index f79d94a..303d5e4 100755 --- a/bp_bin/analyze_seq +++ b/bp_bin/analyze_seq @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'seq' +require 'maasha/biopieces' +require 'maasha/seq' require 'pp' casts = [] diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba index 43434e3..da2f4da 100755 --- a/bp_bin/assemble_seq_idba +++ b/bp_bin/assemble_seq_idba @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet index 85c5fa8..c3e25f3 100755 --- a/bp_bin/assemble_seq_velvet +++ b/bp_bin/assemble_seq_velvet @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'fasta' +require 'maasha/biopieces' +require 'maasha/fasta' class Velvet def initialize(directory, sequence_file, verbose) diff --git a/bp_bin/bin_vals b/bp_bin/bin_vals index 42fb7d6..5f1fd05 100755 --- a/bp_bin/bin_vals +++ b/bp_bin/bin_vals @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil} diff --git a/bp_bin/calc_N50 b/bp_bin/calc_N50 index a97fe08..38de308 100755 --- a/bp_bin/calc_N50 +++ b/bp_bin/calc_N50 @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' require 'pp' casts = [] diff --git a/bp_bin/clip_adaptor b/bp_bin/clip_adaptor index 4399743..2056f2d 100755 --- a/bp_bin/clip_adaptor +++ b/bp_bin/clip_adaptor @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] diff --git a/bp_bin/clip_seq b/bp_bin/clip_seq index c2f9d8e..f26e10b 100755 --- a/bp_bin/clip_seq +++ b/bp_bin/clip_seq @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq index 9fe81e9..03e8ec9 100755 --- a/bp_bin/digest_seq +++ b/bp_bin/digest_seq @@ -29,9 +29,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/find_adaptor b/bp_bin/find_adaptor index e1ac8f3..aa1a014 100755 --- a/bp_bin/find_adaptor +++ b/bp_bin/find_adaptor @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'seq' +require 'maasha/biopieces' +require 'maasha/seq' def disambiguate(adaptor) adaptor_disamb = adaptor.dup diff --git a/bp_bin/find_genes b/bp_bin/find_genes index 367b976..b365ab2 100755 --- a/bp_bin/find_genes +++ b/bp_bin/find_genes @@ -29,9 +29,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/find_homopolymers b/bp_bin/find_homopolymers index ba9d639..5c9cd24 100755 --- a/bp_bin/find_homopolymers +++ b/bp_bin/find_homopolymers @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'seq' +require 'maasha/biopieces' +require 'maasha/seq' require 'pp' casts = [] diff --git a/bp_bin/find_mids b/bp_bin/find_mids index 73bbfb6..81015f6 100755 --- a/bp_bin/find_mids +++ b/bp_bin/find_mids @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' require 'pp' MID_LEN = 10 diff --git a/bp_bin/join_seq b/bp_bin/join_seq index 6abc8c8..de80ad2 100755 --- a/bp_bin/join_seq +++ b/bp_bin/join_seq @@ -28,9 +28,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'fasta' -require 'seq' +require 'maasha/biopieces' +require 'maasha/fasta' +require 'maasha/seq' casts = [] diff --git a/bp_bin/kmer_freq b/bp_bin/kmer_freq index 733eed3..7e412d8 100755 --- a/bp_bin/kmer_freq +++ b/bp_bin/kmer_freq @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'seq' +require 'maasha/biopieces' +require 'maasha/seq' require 'pp' casts = [] diff --git a/bp_bin/length_seq b/bp_bin/length_seq index e3e6b09..0152ef4 100755 --- a/bp_bin/length_seq +++ b/bp_bin/length_seq @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] diff --git a/bp_bin/mask_seq b/bp_bin/mask_seq index 20395c4..f29b68f 100755 --- a/bp_bin/mask_seq +++ b/bp_bin/mask_seq @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' ILLUMINA_BASE = 64 diff --git a/bp_bin/pcr_seq b/bp_bin/pcr_seq index d3ce39a..df97f20 100755 --- a/bp_bin/pcr_seq +++ b/bp_bin/pcr_seq @@ -29,9 +29,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'fasta' -require 'seq' +require 'maasha/biopieces' +require 'maasha/fasta' +require 'maasha/seq' require 'pp' class Pcr diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores index 4ddd7b3..fd44149 100755 --- a/bp_bin/plot_scores +++ b/bp_bin/plot_scores @@ -25,7 +25,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' require 'gnuplot' require 'pp' diff --git a/bp_bin/progress_meter b/bp_bin/progress_meter index b5e0c1c..7678d37 100755 --- a/bp_bin/progress_meter +++ b/bp_bin/progress_meter @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] casts << {:long=>'no_stream', :short => 'x', :type => 'flag', :mandatory => false, :default => nil, :allowed => nil, :disallowed => nil} diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta index c0f9426..9b77008 100755 --- a/bp_bin/read_fasta +++ b/bp_bin/read_fasta @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq index fd88bf0..063edd6 100755 --- a/bp_bin/read_fastq +++ b/bp_bin/read_fastq @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/read_genbank b/bp_bin/read_genbank index 6e471bb..1ab92e4 100755 --- a/bp_bin/read_genbank +++ b/bp_bin/read_genbank @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/read_sff b/bp_bin/read_sff index a14048e..6e5febd 100755 --- a/bp_bin/read_sff +++ b/bp_bin/read_sff @@ -28,8 +28,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -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} diff --git a/bp_bin/remove_mids b/bp_bin/remove_mids index c42a6c0..a2d1fd8 100755 --- a/bp_bin/remove_mids +++ b/bp_bin/remove_mids @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' require 'pp' MID_LEN = 10 diff --git a/bp_bin/scores_to_dec b/bp_bin/scores_to_dec index ecf2148..c5e7c1e 100755 --- a/bp_bin/scores_to_dec +++ b/bp_bin/scores_to_dec @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' ILLUMINA_BASE = 64 diff --git a/bp_bin/shred_seq b/bp_bin/shred_seq index f9e1a42..86bf321 100755 --- a/bp_bin/shred_seq +++ b/bp_bin/shred_seq @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'seq' +require 'maasha/biopieces' +require 'maasha/seq' require 'pp' class Seq diff --git a/bp_bin/shuffle_records b/bp_bin/shuffle_records index b132229..194cab0 100755 --- a/bp_bin/shuffle_records +++ b/bp_bin/shuffle_records @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] diff --git a/bp_bin/swapcase_seq b/bp_bin/swapcase_seq index cb1989c..60725f5 100755 --- a/bp_bin/swapcase_seq +++ b/bp_bin/swapcase_seq @@ -29,7 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' +require 'maasha/biopieces' casts = [] diff --git a/bp_bin/uclust_seq b/bp_bin/uclust_seq index cbc0bc6..76c5668 100755 --- a/bp_bin/uclust_seq +++ b/bp_bin/uclust_seq @@ -29,8 +29,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'biopieces' -require 'fasta' +require 'maasha/biopieces' +require 'maasha/fasta' class Uclust include Enumerable diff --git a/bp_conf/bashrc b/bp_conf/bashrc index b5eb789..782195e 100644 --- a/bp_conf/bashrc +++ b/bp_conf/bashrc @@ -32,7 +32,7 @@ export PERL5LIB="$PERL5LIB:$BP_PERL" ### 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. diff --git a/code_ruby/Maasha/Rakefile b/code_ruby/Maasha/Rakefile deleted file mode 100644 index 8f5b25f..0000000 --- a/code_ruby/Maasha/Rakefile +++ /dev/null @@ -1,6 +0,0 @@ -require 'rake/testtask' - -Rake::TestTask.new("test") do |t| - t.pattern = "test/test_*.rb" - t.warning = true -end diff --git a/code_ruby/Maasha/lib/doc/Base36.html b/code_ruby/Maasha/lib/doc/Base36.html deleted file mode 100644 index c1078ec..0000000 --- a/code_ruby/Maasha/lib/doc/Base36.html +++ /dev/null @@ -1,316 +0,0 @@ - - - - - - - Class: Base36 - - - - - - - - - - - -
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Base36

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-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). -

-

-en.wikipedia.org/wiki/Base_36 -

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-Method that decodes a base36 string and returns an integer. -

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-    # File base36.rb, line 55
-55:   def self.decode(base36)
-56:     raise Base36Error if base36.empty?
-57: 
-58:     result = 0
-59:     pos    = 0
-60: 
-61:     base36.upcase.reverse.each_char do |char|
-62:       result += ALPH.index(char) * (BASE36 ** pos)
-63:       pos    += 1
-64:     end
-65: 
-66:     return result;
-67:   end
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-Method that encodes an integer into a base36 string that is returned. -

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-    # File base36.rb, line 39
-39:   def self.encode(num)
-40:     raise Base36Error unless num.is_a? Fixnum
-41: 
-42:     base36 = ""
-43: 
-44:     while num > 0
-45:       base36 << ALPH[(num % BASE36)]
-46:       num /= BASE36
-47:     end
-48: 
-49:     base36 << ALPH[0] if num == 0
-50: 
-51:     base36.reverse
-52:   end
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-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 ’—’. -

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-Initialize a Biopiece and write the status to file. Options are for testing -purposes only. -

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-    # File biopieces.rb, line 49
-49:   def initialize(test=nil, input=STDIN, output=STDOUT)
-50:     @test   = test
-51:     @input  = input
-52:     @output = output
-53:   end
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-Open Biopiece input stream if not open and iterate over all Biopiece -records in the stream. -

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-    # File biopieces.rb, line 66
-66:   def each_record
-67:     @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
-68:     return if @in.nil?
-69: 
-70:     record = {}
-71: 
-72:     @in.each_line do |line|
-73:       case line
-74:       when /^([^:]+): (.*)$/
-75:         record[$1.to_sym] = $2
-76:       when /^---$/
-77:         yield record unless record.empty?
-78:         record = {}
-79:       else
-80:         raise "Bad record format: #{line}"
-81:       end
-82:     end
-83: 
-84:     yield record unless record.empty?
-85: 
-86:     self # conventionally
-87:   end
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-     # File biopieces.rb, line 106
-106:   def mktmpdir
-107:     time = Time.now.to_i
-108:     user = ENV["USER"]
-109:     pid  = $$
-110:     path = ENV["BP_TMP"] + "/" + [user, time + pid, pid, "bp_tmp"].join("_")
-111:     Dir.mkdir(path)
-112:     Status.new.set_tmpdir(path)
-113:     path
-114:   end
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-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. -

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-    # File biopieces.rb, line 58
-58:   def parse(argv, cast_list=[], script_path=$0)
-59:     casts          = Casts.new(cast_list)
-60:     option_handler = OptionHandler.new(argv, casts, script_path, @test)
-61:     @options       = option_handler.options_parse
-62:   end
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-Open Biopiece output stream if not open and puts record to the stream. -

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-     # File biopieces.rb, line 92
- 92:   def puts(record)
- 93:     @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
- 94: 
- 95:     record.each do |key,value|
- 96:       @out.print "#{key.to_s}: #{value}\n"
- 97:     end
- 98: 
- 99:     @out.print "---\n"
-100:   end
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-     # File biopieces.rb, line 102
-102:   def to_s
-103:   end
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- - - - diff --git a/code_ruby/Maasha/lib/doc/BitArray.html b/code_ruby/Maasha/lib/doc/BitArray.html deleted file mode 100644 index 44a12d4..0000000 --- a/code_ruby/Maasha/lib/doc/BitArray.html +++ /dev/null @@ -1,869 +0,0 @@ - - - - - - - Class: BitArray - - - - - - - - - - - -
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BitArray

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-Class containing methods for creating and manipulating a bit array. -

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Attributes

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-Method to initialize a new bit array of a given size. -

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-
-    # File bitarray.rb, line 35
-35:   def initialize(size)
-36:     @size        = size
-37:     @byte_array  = init_byte_array
-38:     @count_array = init_count_array
-39:   end
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Public Instance Methods

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- - &(ba) - click to toggle source - -
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-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 -

- - - -
-
-    # File bitarray.rb, line 76
-76:   def &(ba)
-77:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
-78: 
-79:     result = BitArray.new(ba.size)
-80: 
-81:     (0 ... ba.byte_array.size).each do |byte|
-82:       result.byte_array[byte] = (self.byte_array[byte].ord & ba.byte_array[byte].ord).chr
-83:     end
-84: 
-85:     result
-86:   end
-
- -
- - - - -
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- - -
- - ^(ba) - click to toggle source - -
- -
- -

-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 -

- - - -
-
-     # File bitarray.rb, line 106
-106:   def ^(ba)
-107:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
-108: 
-109:     result = BitArray.new(ba.size)
-110: 
-111:     (0 ... ba.byte_array.size).each do |byte|
-112:       result.byte_array[byte] = (self.byte_array[byte].ord ^ ba.byte_array[byte].ord).chr
-113:     end
-114: 
-115:     result
-116:   end
-
- -
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- - bit_set(pos) - click to toggle source - -
- -
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-Method to set a bit to 1 at a given position in the bit array. -

- - - -
-
-    # File bitarray.rb, line 42
-42:   def bit_set(pos)
-43:     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
-44:     raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
-45: 
-46:     @byte_array[byte_pos(pos)] = (@byte_array[byte_pos(pos)].ord | bit_pos(pos)).chr
-47:   end
-
- -
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- - bit_set?(pos) - click to toggle source - -
- -
- -

-Method to check if a bit at a given position in the bit array is set. -

- - - -
-
-    # File bitarray.rb, line 50
-50:   def bit_set?(pos)
-51:     raise BitArrayError, "Position #{pos} must be an integer."              unless pos.is_a? Fixnum
-52:     raise BitArrayError, "Position #{pos} outside of range: 0 ... #{@size}" unless (0 ... @size ).include? pos
-53: 
-54:     (@byte_array[byte_pos(pos)].ord & bit_pos(pos)) != 0
-55:   end
-
- -
- - - - -
- - -
- - -
- - bits_off() - click to toggle source - -
- -
- -

-Method that returns the number of bits set “off” in a bit -array. -

- - - -
-
-    # File bitarray.rb, line 69
-69:   def bits_off
-70:     @size - bits_on
-71:   end
-
- -
- - - - -
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- - -
- - bits_on() - click to toggle source - -
- -
- -

-Method that returns the number of bits set “on” in a bit array. -

- - - -
-
-    # File bitarray.rb, line 58
-58:   def bits_on 
-59:     bits_on = 0
-60: 
-61:     (0 ... self.byte_array.size).each do |byte|
-62:       bits_on += @count_array[self.byte_array[byte].ord]
-63:     end
-64: 
-65:     bits_on
-66:   end
-
- -
- - - - -
- - -
- - -
- - to_s() - click to toggle source - -
- -
- -

-Method to convert a bit array to a string. -

- - - -
-
-     # File bitarray.rb, line 119
-119:   def to_s
-120:     string = ""
-121: 
-122:     (0 ... @size).each do |pos|
-123:       if self.bit_set? pos 
-124:         string << "1"
-125:       else
-126:         string << "0"
-127:       end
-128:     end
-129: 
-130:     string
-131:   end
-
- -
- - - - -
- - -
- - -
- - |(ba) - click to toggle source - -
- -
- -

-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 -

- - - -
-
-     # File bitarray.rb, line 91
- 91:   def |(ba)
- 92:     raise BitArrayError, "uneven size of bit arrays: #{self.size} != #{ba.size}" if self.size != ba.size
- 93: 
- 94:     result = BitArray.new(ba.size)
- 95: 
- 96:     (0 ... ba.byte_array.size).each do |byte|
- 97:       result.byte_array[byte] = (self.byte_array[byte].ord | ba.byte_array[byte].ord).chr
- 98:     end
- 99: 
-100:     result
-101:   end
-
- -
- - - - -
- - -
- -
-

Private Instance Methods

- - -
- - -
- - bit_pos(pos) - click to toggle source - -
- -
- -

-Method that returns the bit position in a byte. -

- - - -
-
-     # File bitarray.rb, line 177
-177:   def bit_pos(pos)
-178:     1 << (BitsInChar - 1 - (pos % BitsInChar))
-179:   end
-
- -
- - - - -
- - -
- - -
- - bits_in_char(char) - click to toggle source - -
- -
- -

-Method that returns the number of set bits in a char. -

- - - -
-
-     # File bitarray.rb, line 161
-161:   def bits_in_char(char)
-162:     bits = 0
-163: 
-164:     (0 ... BitsInChar).each do |pos|
-165:       bits += 1 if ((char & bit_pos(pos)) != 0)
-166:     end
-167: 
-168:     bits
-169:   end
-
- -
- - - - -
- - -
- - -
- - byte_pos(pos) - click to toggle source - -
- -
- -

-Method that returns the byte position in the byte array for a given bit -position. -

- - - -
-
-     # File bitarray.rb, line 172
-172:   def byte_pos(pos)
-173:     pos / BitsInChar
-174:   end
-
- -
- - - - -
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- - init_byte_array() - click to toggle source - -
- -
- -

-Method to initialize the byte array (string) that constitutes the bit -array. -

- - - -
-
-     # File bitarray.rb, line 138
-138:   def init_byte_array
-139:     raise BitArrayError, "Size must be an integer, not #{@size}" unless @size.is_a? Fixnum
-140:     raise BitArrayError, "Size must be positive, not #{@size}"   unless @size > 0
-141: 
-142:     byte_array = ""
-143:     byte_array << 0.chr * (((@size - 1) / BitsInChar) + 1)
-144: 
-145:     byte_array
-146:   end
-
- -
- - - - -
- - -
- - -
- - init_count_array() - click to toggle source - -
- -
- -

-Method that returns an array where the element index value is the number of -bits set for that index value. -

- - - -
-
-     # File bitarray.rb, line 150
-150:   def init_count_array
-151:     count_array = []
-152: 
-153:     (0 ... (2 ** BitsInChar)).each do |i|
-154:       count_array << bits_in_char(i)
-155:     end
-156: 
-157:     count_array
-158:   end
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Generated with the Darkfish - Rdoc Generator 1.1.6.

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-Error class for all exceptions to do with BitArray. -

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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/Boulder.html b/code_ruby/Maasha/lib/doc/Boulder.html deleted file mode 100644 index b1af1ca..0000000 --- a/code_ruby/Maasha/lib/doc/Boulder.html +++ /dev/null @@ -1,361 +0,0 @@ - - - - - - - Class: Boulder - - - - - - - - - - - -
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Boulder

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-Class to manipulate boulder records - Lincoln Steins own YAML like format: -stein.cshl.org/boulder/docs/Boulder.html -

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Public Class Methods

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-Initialize a Boulder object. Options are for -testing purposes only. -

- - - -
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-    # File boulder.rb, line 39
-39:   def initialize(input=STDIN, output=STDOUT)
-40:     @input  = input
-41:     @output = output
-42:   end
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-    # File boulder.rb, line 44
-44:   def each
-45:     while not @input.eof? do
-46:       block = @input.gets(SEP)
-47:       raise BoulderError, "Missing record seperator" unless block =~ /#{SEP}$/
-48: 
-49:       record = {}
-50: 
-51:       block.chomp(SEP).each_line do |line|
-52:         key, val = line.chomp.split('=', 2)
-53: 
-54:         raise BoulderError, "Missing key/value seperator" if val.nil?
-55:         raise BoulderError, "Missing key"                 if key.empty?
-56:         raise BoulderError, "Missing value"               if val.empty?
-57: 
-58:         record[key.to_sym] = val
-59:       end
-60: 
-61:       yield record
-62:     end
-63:   end
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-Method that converts and returns a hash record as a Boulder string. -

- - - -
-
-    # File boulder.rb, line 67
-67:   def to_boulder(record)
-68:     str = ""
-69: 
-70:     record.each_pair do |key, val|
-71:       str << "#{key}=#{val}\n"
-72:     end
-73: 
-74:     str << "=\n"
-75: 
-76:     str
-77:   end
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-Error class for all exceptions to do with Boulder. -

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-Error class for all exceptions to do with option casts. -

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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. -

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-Initialize cast object with an optional options cast list to which -ubiquitous casts are added after which all casts are checked. -

- - - -
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-     # File biopieces.rb, line 132
-132:   def initialize(cast_list=[])
-133:     @cast_list = cast_list
-134:     ubiquitous
-135:     check
-136:     long_to_sym
-137:     self.push *@cast_list
-138:   end
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-Check integrity of the casts. -

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-     # File biopieces.rb, line 151
-151:   def check
-152:     check_keys
-153:     check_values
-154:     check_duplicates
-155:   end
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-Check cast for duplicate long or short options names. -

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-     # File biopieces.rb, line 237
-237:   def check_duplicates
-238:     check_hash = {}
-239:     @cast_list.each do |cast|
-240:       raise CastError, "Duplicate argument: '--#{cast[:long]}'" if check_hash.has_key? cast[:long]
-241:       raise CastError, "Duplicate argument: '-#{cast[:short]}'" if check_hash.has_key? cast[:short]
-242:       check_hash[cast[:long]]  = true
-243:       check_hash[cast[:short]] = true
-244:     end
-245:   end
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-Check if all mandatory keys are present in casts and raise if not. -

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-     # File biopieces.rb, line 158
-158:   def check_keys
-159:     @cast_list.each do |cast|
-160:       MANDATORY.each do |mandatory|
-161:         raise CastError, "Missing symbol in cast: '#{mandatory.to_sym}'" unless cast.has_key? mandatory.to_sym
-162:       end
-163:     end
-164:   end
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-Check if values to allowed are legal and raise if not. -

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-     # File biopieces.rb, line 223
-223:   def check_val_allowed(cast)
-224:     unless cast[:allowed].is_a? String or cast[:allowed].nil?
-225:       raise CastError, "Illegal cast of allowed: '#{cast[:allowed]}'"
-226:     end
-227:   end
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- -
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-Check if values to default are legal and raise if not. -

- - - -
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-     # File biopieces.rb, line 213
-213:   def check_val_default(cast)
-214:     unless cast[:default].nil?          or
-215:            cast[:default].is_a? String  or
-216:            cast[:default].is_a? Integer or
-217:            cast[:default].is_a? Float
-218:       raise CastError, "Illegal cast of default: '#{cast[:default]}'"
-219:     end
-220:   end
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-Check if values to disallowed are legal and raise if not. -

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-     # File biopieces.rb, line 230
-230:   def check_val_disallowed(cast)
-231:     unless cast[:disallowed].is_a? String or cast[:disallowed].nil?
-232:       raise CastError, "Illegal cast of disallowed: '#{cast[:disallowed]}'"
-233:     end
-234:   end
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-Check if the values to long are legal and raise if not. -

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-     # File biopieces.rb, line 180
-180:   def check_val_long(cast)
-181:     unless cast[:long].is_a? String and cast[:long].length > 1
-182:       raise CastError, "Illegal cast of long: '#{cast[:long]}'"
-183:     end
-184:   end
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-     # File biopieces.rb, line 206
-206:   def check_val_mandatory(cast)
-207:     unless cast[:mandatory] == true or cast[:mandatory] == false
-208:       raise CastError, "Illegal cast of mandatory: '#{cast[:mandatory]}'"
-209:     end
-210:   end
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-     # File biopieces.rb, line 187
-187:   def check_val_short(cast)
-188:     unless cast[:short].is_a? String and cast[:short].length == 1
-189:       raise CastError, "Illegal cast of short: '#{cast[:short]}'"
-190:     end
-191:   end
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-     # File biopieces.rb, line 194
-194:   def check_val_type(cast)
-195:     type_hash = {}
-196:     TYPES.each do |type|
-197:       type_hash[type] = true
-198:     end
-199: 
-200:     unless type_hash.has_key? cast[:type]
-201:       raise CastError, "Illegal cast of type: '#{cast[:type]}'"
-202:     end
-203:   end
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-     # File biopieces.rb, line 167
-167:   def check_values
-168:     @cast_list.each do |cast|
-169:       check_val_long(cast)
-170:       check_val_short(cast)
-171:       check_val_type(cast)
-172:       check_val_mandatory(cast)
-173:       check_val_default(cast)
-174:       check_val_allowed(cast)
-175:       check_val_disallowed(cast)
-176:     end
-177:   end
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- - - -
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-     # File biopieces.rb, line 248
-248:   def long_to_sym
-249:     @cast_list.each do |cast|
-250:       cast[:long] = cast[:long].to_sym
-251:     end
-252:   end
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-Add ubiquitous options casts. -

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-     # File biopieces.rb, line 143
-143:   def ubiquitous
-144:     @cast_list << {:long=>'help',       :short=>'?', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-145:     @cast_list << {:long=>'stream_in',  :short=>'I', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-146:     @cast_list << {:long=>'stream_out', :short=>'O', :type=>'file',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-147:     @cast_list << {:long=>'verbose',    :short=>'v', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-148:   end
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-Initialize a digest object with the following arguments: -

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-    # File digest.rb, line 37
-37:   def initialize(seq, pattern, cut_pos)
-38:     @seq     = seq
-39:     @pattern = disambiguate(pattern)
-40:     @cut_pos = cut_pos
-41:     @offset  = 0
-42:   end
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-Method to get the next digestion product from a sequence. -

- - - -
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-    # File digest.rb, line 45
-45:   def each
-46:     @seq.seq.upcase.scan @pattern do
-47:       pos = $`.length + @cut_pos - 1
-48:      
-49:       if pos >= 0 and pos < @seq.length - 2
-50:         seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{pos}]", @seq.seq[@offset .. pos], @seq.type)
-51: 
-52:         yield seq
-53:       end
-54: 
-55:       @offset = pos + 1
-56:     end
-57: 
-58:     if @offset < 0
-59:       @offset = 0
-60:     elsif @offset > @seq.length
-61:       @offset = 0
-62:     end
-63: 
-64:     seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]", @seq.seq[@offset .. @seq.length], @seq.type)
-65: 
-66:     yield seq
-67: 
-68:     self # conventionally
-69:   end
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Private Instance Methods

- - -
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-Method that returns a regexp object with a restriction enzyme pattern with -ambiguity codes substituted to the appropriate regexp. -

- - - -
-
-     # File digest.rb, line 76
- 76:   def disambiguate(pattern)
- 77:     ambiguity = {
- 78:       'A' => "A",
- 79:       'T' => "T",
- 80:       'U' => "T",
- 81:       'C' => "C",
- 82:       'G' => "G",
- 83:       'M' => "[AC]",
- 84:       'R' => "[AG]",
- 85:       'W' => "[AT]",
- 86:       'S' => "[CG]",
- 87:       'Y' => "[CT]",
- 88:       'K' => "[GT]",
- 89:       'V' => "[ACG]",
- 90:       'H' => "[ACT]",
- 91:       'D' => "[AGT]",
- 92:       'B' => "[CGT]",
- 93:       'N' => "[GATC]"
- 94:     }
- 95: 
- 96:     new_pattern = ""
- 97: 
- 98:     pattern.upcase.each_char do |char|
- 99:       if ambiguity.has_key? char
-100:         new_pattern << ambiguity[char]
-101:       else
-102:         raise DigestError, "Could not disambiguate residue: #{char}"
-103:       end
-104:     end
-105: 
-106:     Regexp.new(new_pattern)
-107:   end
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-Error class for all exceptions to do with Digest. -

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- - - - diff --git a/code_ruby/Maasha/lib/doc/Fasta.html b/code_ruby/Maasha/lib/doc/Fasta.html deleted file mode 100644 index 65ce1bb..0000000 --- a/code_ruby/Maasha/lib/doc/Fasta.html +++ /dev/null @@ -1,308 +0,0 @@ - - - - - - - Class: Fasta - - - - - - - - - - - -
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-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. -

- - - -
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-    # File fasta.rb, line 34
-34:   def get_entry
-35:     block = @io.gets($/ + '>')
-36:     return nil if block.nil?
-37: 
-38:     block.chomp!($/ + '>')
-39: 
-40:     (seq_name, seq) = block.split($/, 2)
-41: 
-42:     raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
-43: 
-44:     entry          = Seq.new
-45:     entry.type     = @type.nil? ? nil : @type.downcase
-46:     entry.seq      = seq.gsub(/\s/, '')
-47:     entry.seq_name = seq_name.sub(/^>/, '').rstrip
-48: 
-49:     raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
-50:     raise FastaError, "Bad FASTA format" if entry.seq.empty?
-51: 
-52:     entry
-53:   end
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- -
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-TODO - this should be some custom to_s method instead. -

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-    # File fasta.rb, line 56
-56:   def puts(record)
-57:     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
-58:       @io.print ">#{record[:SEQ_NAME]}\n"
-59:       @io.print "#{record[:SEQ]}\n"
-60:     end
-61:   end
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-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. -

- - - -
-
-    # File fastq.rb, line 34
-34:   def get_entry
-35:     begin
-36:       seq_name       = @io.gets.chomp!
-37:       seq            = @io.gets.chomp!
-38:       qual_name      = @io.gets.chomp!
-39:       qual           = @io.gets.chomp!
-40: 
-41:       entry          = Seq.new
-42:       entry.type     = @type.nil? ? nil : @type.downcase
-43:       entry.seq      = seq
-44:       entry.seq_name = seq_name[1 .. seq_name.length]
-45:       entry.qual     = qual
-46: 
-47:       entry
-48:     rescue
-49:       nil
-50:     end
-51:   end
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-    # File fastq.rb, line 54
-54:   def puts(record)
-55:     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
-56:       @io.print ">#{record[:SEQ_NAME]}\n"
-57:       @io.print "#{record[:SEQ]}\n"
-58:     end
-59:   end
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-58:   def initialize(io, type=nil)
-59:     @io   = io
-60:     @type = type
-61:   end
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-35:   def self.open(*args)
-36:     args = *args
-37:     file = args.first
-38: 
-39:     if file == "-"
-40:       ios = self.new(STDIN)
-41:     elsif File.pipe? file
-42:       ios = self.new(File.open(*args))
-43:     else
-44:       ios = self.zopen(*args)
-45:     end
-46: 
-47:     if block_given?
-48:       begin
-49:         yield ios
-50:       ensure
-51:         ios.close
-52:       end
-53:     else
-54:       return ios
-55:     end
-56:   end
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-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. -

- - - -
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-    # File filesys.rb, line 79
-79:   def self.zopen(*args)
-80:     ios = File.open(*args)
-81: 
-82:     begin
-83:       ios = Zlib::GzipReader.new(ios)
-84:     rescue
-85:       ios.rewind
-86:     end
-87: 
-88:     self.new(ios)
-89:   end
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-Method to close ios. -

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-    # File filesys.rb, line 64
-64:   def close
-65:     @io.close
-66:   end
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-69:   def each
-70:     while entry = get_entry do
-71:       yield entry
-72:     end
-73:   end
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-32:   def initialize(io)
-33:     @io      = io
-34:     @entry   = []
-35:   end
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-Iterator method for parsing Genbank entries. -

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-    # File genbank.rb, line 38
-38:   def each(hash_keys, hash_feats, hash_quals)
-39:     while @entry = get_entry do
-40:       keys = get_keys(hash_keys)
-41:       seq  = get_seq
-42: 
-43:       features = GenbankFeatures.new(@entry, hash_feats, hash_quals)
-44: 
-45:       features.each do |record|
-46:         keys.each_pair { |key,val| record[key] = val }
-47: 
-48:                                 loc = Locator.new(record[:LOCATOR], seq)
-49:                                 record[:SEQ]     = loc.subseq.seq
-50:         record[:SEQ_LEN] = loc.subseq.length
-51:                                 record[:STRAND]  = loc.strand
-52:                                 record[:S_BEG]   = loc.s_beg
-53:                                 record[:S_END]   = loc.s_end
-54: 
-55:         yield record
-56:       end
-57:     end
-58:   end
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-Method to get the next Genbank entry form an ios -and return this. -

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-    # File genbank.rb, line 63
-63:   def get_entry
-64:     block = @io.gets("//" + $/)
-65:     return nil if block.nil?
-66: 
-67:     block.chomp!("//" + $/ )
-68: 
-69:     entry = block.split $/
-70: 
-71:     return nil if entry.empty?
-72: 
-73:     entry
-74:   end
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-Method to get the base keys from Genbank entry -and return these in a hash. -

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-     # File genbank.rb, line 93
- 93:   def get_keys(hash_keys)
- 94:     keys = {}
- 95:     i    = 0
- 96:     j    = 0
- 97: 
- 98:     while @entry[i] and @entry[i] !~ /^FEATURES/
- 99:       if @entry[i] =~ /^\s{0,3}([A-Z]{2})/
-100:         if want_key?(hash_keys, $1)
-101:           j = i + 1
-102: 
-103:           key, val = @entry[i].lstrip.split(/\s+/, 2)
-104: 
-105:           while @entry[j] and @entry[j] !~ /^\s{0,3}[A-Z]/
-106:             val << @entry[j].lstrip
-107:             j += 1
-108:           end
-109: 
-110:           if keys[key.to_sym]
-111:             keys[key.to_sym] << ";" + val
-112:           else
-113:             keys[key.to_sym] = val
-114:           end
-115:         end
-116:       end
-117: 
-118:       j > i ? i = j : i += 1
-119:     end
-120: 
-121:     keys
-122:   end
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-Method to get the DNA sequence from a Genbank -entry and return this as a Seq object. -

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-    # File genbank.rb, line 78
-78:   def get_seq
-79:     i = @entry.size
-80:     j = i - 1
-81: 
-82:     while @entry[j] and @entry[j] !~ /^[A-Z]/
-83:       j -= 1
-84:     end
-85: 
-86:     seq = @entry[j + 1 .. i].join.delete(" 0123456789")
-87: 
-88:     Seq.new(nil, seq, "dna") if seq
-89:   end
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-124:   def want_key?(hash_keys, key)
-125:     if hash_keys
-126:       if hash_keys[key.to_sym]
-127:         return true
-128:       else
-129:         return false
-130:       end
-131:     else
-132:       return true
-133:     end
-134:   end
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-Error class for all exceptions to do with Genbank. -

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-     # File genbank.rb, line 141
-141:   def initialize(entry, hash_feats, hash_quals)
-142:     @entry      = entry
-143:     @hash_feats = hash_feats
-144:     @hash_quals = hash_quals
-145:   end
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-     # File genbank.rb, line 147
-147:   def each
-148:     while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
-149:       if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
-150:         if want_feat? $1
-151:           record = {}
-152: 
-153:           feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
-154: 
-155:           @@j = @@i + 1
-156: 
-157:           while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
-158:             loc << @entry[@@j].lstrip
-159:             @@j += 1
-160:           end
-161: 
-162:           get_quals.each_pair { |k,v|
-163:             record[k.upcase.to_sym] = v
-164:           }
-165: 
-166:           record[:FEATURE] = feat
-167:           record[:LOCATOR] = loc
-168: 
-169:           yield record
-170:         end
-171:       end
-172: 
-173:       @@j > @@i ? @@i = @@j : @@i += 1
-174:     end
-175:   end
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-     # File genbank.rb, line 179
-179:   def get_quals
-180:     quals = {}
-181:     k     = 0
-182: 
-183:     while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
-184:       if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
-185:         qual = $1
-186:         val  = $2
-187: 
-188:         if want_qual? qual
-189:           k = @@j + 1
-190: 
-191:           while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
-192:             val << @entry[k].lstrip.chomp('"')
-193:             k += 1
-194:           end
-195: 
-196:           if quals[qual]
-197:             quals[qual] << ";" + val
-198:           else
-199:             quals[qual] = val
-200:           end
-201:         end
-202:       end
-203: 
-204:       k > @@j ? @@j = k : @@j += 1
-205:     end
-206: 
-207:     quals
-208:   end
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-     # File genbank.rb, line 210
-210:   def want_feat?(feat)
-211:     if @hash_feats
-212:       if @hash_feats[feat.upcase.to_sym]
-213:         return true
-214:       else
-215:         return false
-216:       end
-217:     else
-218:       return true
-219:     end
-220:   end
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-     # File genbank.rb, line 222
-222:   def want_qual?(qual)
-223:     if @hash_quals
-224:       if @hash_quals[qual.upcase.to_sym]
-225:         return true
-226:       else
-227:         return false
-228:       end
-229:     else
-230:       return true
-231:     end
-232:   end
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-     # File genbank.rb, line 242
-242:   def initialize(locator, seq)
-243:     @locator = locator
-244:     @seq     = seq
-245:     @subseq  = Seq.new(nil, "", "dna")
-246:     parse_locator(locator)
-247:   end
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-     # File genbank.rb, line 257
-257:   def s_beg
-258:     if @locator =~ /(\d+)/
-259:       return $1.to_i - 1
-260:     end
-261:   end
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-     # File genbank.rb, line 263
-263:   def s_end
-264:     if @locator.reverse =~ /(\d+)/
-265:       return $1.reverse.to_i - 1
-266:     end
-267:   end
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-     # File genbank.rb, line 249
-249:   def strand
-250:     if @locator.match("complement")
-251:       return "-"
-252:     else
-253:       return "+"
-254:     end
-255:   end
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- - balance_parens?(locator) - click to toggle source - -
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-     # File genbank.rb, line 342
-342:   def balance_parens?(locator)
-343:     parens = 0
-344: 
-345:     locator.each_char do |char|
-346:       case char
-347:       when '(' then parens += 1
-348:       when ')' then parens -= 1
-349:       end
-350:     end
-351: 
-352:     if parens == 0
-353:       return true
-354:     else
-355:       return false
-356:     end
-357:   end
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- -

-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). -

- - - -
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-     # File genbank.rb, line 279
-279:   def parse_locator(locator, join = nil, comp = nil, order = nil)
-280:     intervals = locator.split(",")
-281: 
-282:     unless balance_parens?(intervals.first)   # locator includes a join/comp/order of several ranges
-283:       case locator
-284:       when /^join\((.*)\)$/
-285:         locator = $1
-286:         join     = true
-287:       when /^complement\((.*)\)$/
-288:         locator = $1
-289:         comp     = true
-290:       when /^order\((.*)\)$/
-291:         locator = $1
-292:         order    = true
-293:       end
-294: 
-295:       parse_locator(locator, join, comp, order)
-296:     else
-297:       intervals.each do |interval|
-298:         case interval
-299:         when /^join\((.*)\)$/
-300:           locator = $1
-301:           join    = true
-302:           parse_locator(locator, join, comp, order)
-303:         when /^complement\((.*)\)$/
-304:           locator = $1
-305:           comp    = true
-306:           parse_locator(locator, join, comp, order)
-307:         when /^order\((.*)\)$/
-308:           locator = $1
-309:           order   = true
-310:           parse_locator(locator, join, comp, order)
-311:         when /^[<>]?(\d+)[^\d]+(\d+)$/
-312:           int_beg = $1.to_i - 1
-313:           int_end = $2.to_i - 1
-314: 
-315:           newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
-316: 
-317:                                         unless newseq.seq.nil?
-318:                                                 newseq.revcomp if comp
-319: 
-320:                                                 @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
-321:                                         end
-322:         when /^(\d+)$/
-323:           pos = $1.to_i - 1
-324: 
-325:           newseq = Seq.new(nil, @seq.seq[pos], "dna")
-326: 
-327:                                         unless newseq.seq.nil?
-328:                 newseq.revcomp if comp 
-329: 
-330:                 @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
-331:                                         end
-332:         else
-333:           $stderr.puts "WARNING: Could not match locator -> #{locator}";
-334:           @subseq.seq << ""
-335:         end
-336:       end
-337:     end
-338: 
-339:     return @subseq
-340:   end
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-Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table -locators. -

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-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. -

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-266:   def initialize(argv, casts, script_path, test=nil)
-267:     @argv        = argv
-268:     @casts       = casts
-269:     @script_path = script_path
-270:     @test        = test
-271:   end
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-Check all options according to casts. -

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-     # File biopieces.rb, line 407
-407:   def options_check
-408:     @casts.each do |cast|
-409:       options_check_mandatory(cast)
-410:       options_check_int(cast)
-411:       options_check_uint(cast)
-412:       options_check_file(cast)
-413:       options_check_files(cast)
-414:       options_check_dir(cast)
-415:       options_check_allowed(cast)
-416:       options_check_disallowed(cast)
-417:     end
-418:   end
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-Check options and raise unless allowed. -

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-     # File biopieces.rb, line 470
-470:   def options_check_allowed(cast)
-471:     if cast[:allowed] and @options.has_key? cast[:long]
-472:       allowed_hash = {}
-473:       cast[:allowed].split(',').each { |a| allowed_hash[a.to_s] = 1 }
-474:   
-475:       raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed" unless allowed_hash.has_key? @options[cast[:long]].to_s
-476:     end
-477:   end
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-463:   def options_check_dir(cast)
-464:     if cast[:type] == 'dir!' and @options.has_key? cast[:long]
-465:       raise ArgumentError, "No such directory: '#{@options[cast[:long]]}'" unless File.directory? @options[cast[:long]]
-466:     end
-467:   end
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-480:   def options_check_disallowed(cast)
-481:     if cast[:disallowed] and @options.has_key? cast[:long]
-482:       cast[:disallowed].split(',').each do |val|
-483:         raise ArgumentError, "Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed" if val.to_s == @options[cast[:long]].to_s
-484:       end
-485:     end
-486:   end
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-446:   def options_check_file(cast)
-447:     if cast[:type] == 'file!' and @options.has_key? cast[:long]
-448:       raise ArgumentError, "No such file: '#{@options[cast[:long]]}'" unless File.file? @options[cast[:long]]
-449:     end
-450:   end
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-     # File biopieces.rb, line 453
-453:   def options_check_files(cast)
-454:     if cast[:type] == 'files!' and @options.has_key? cast[:long]
-455:       @options[cast[:long]].each do |path|
-456:         next if path == "-"
-457:         raise ArgumentError, "File not readable: '#{path}'" unless File.readable? path
-458:       end
-459:     end
-460:   end
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- -

-Check int type option and raise if not an integer. -

- - - -
-
-     # File biopieces.rb, line 428
-428:   def options_check_int(cast)
-429:     if cast[:type] == 'int' and @options.has_key? cast[:long]
-430:       unless @options[cast[:long]].is_a? Integer
-431:         raise ArgumentError, "Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"
-432:       end
-433:     end
-434:   end
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-Check if a mandatory option is set and raise if it isn’t. -

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-     # File biopieces.rb, line 421
-421:   def options_check_mandatory(cast)
-422:     if cast[:mandatory]
-423:       raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
-424:     end
-425:   end
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-Check uint type option and raise if not an unsinged integer. -

- - - -
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-     # File biopieces.rb, line 437
-437:   def options_check_uint(cast)
-438:     if cast[:type] == 'uint' and @options.has_key? cast[:long]
-439:       unless @options[cast[:long]].is_a? Integer and @options[cast[:long]] >= 0
-440:         raise ArgumentError, "Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"
-441:       end
-442:     end
-443:   end
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-Set default options value from cast unless a value is set. -

- - - -
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-     # File biopieces.rb, line 374
-374:   def options_default
-375:     @casts.each do |cast|
-376:       if cast[:default]
-377:         @options[cast[:long]] = cast[:default] unless @options.has_key? cast[:long]
-378:       end
-379:     end
-380:   end
-
- -
- - - - -
- - -
- - -
- - options_glob() - click to toggle source - -
- -
- -

-Expands glob expressions to a full list of paths. Examples: -“*.fna” or “foo.fna,*.fna” or -“foo.fna,/bar/*.fna“ -

- - - -
-
-     # File biopieces.rb, line 384
-384:   def options_glob
-385:     @casts.each do |cast|
-386:       if cast[:type] == 'files' or cast[:type] == 'files!'
-387:         if @options.has_key? cast[:long]
-388:           files = []
-389:         
-390:           @options[cast[:long]].each do |path|
-391:             if path.include? "*"
-392:               Dir.glob(path).each do |file|
-393:                 files << file if File.file? file
-394:               end
-395:             else
-396:               files << path
-397:             end
-398:           end
-399: 
-400:           @options[cast[:long]] = files
-401:         end
-402:       end
-403:     end
-404:   end
-
- -
- - - - -
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- - -
- - options_parse() - click to toggle source - -
- -
- -

-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. -

- - - -
-
-     # File biopieces.rb, line 276
-276:   def options_parse
-277:     @options = {}
-278: 
-279:     option_parser = OptionParser.new do |option|
-280:       @casts.each do |cast|
-281:         case cast[:type]
-282:         when 'flag'
-283:           option.on("-#{cast[:short]}", "--#{cast[:long]}") do |o|
-284:             @options[cast[:long]] = o
-285:           end
-286:         when 'float'
-287:           option.on("-#{cast[:short]}", "--#{cast[:long]} F", Float) do |f|
-288:             @options[cast[:long]] = f
-289:           end
-290:         when 'string'
-291:           option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
-292:             @options[cast[:long]] = s.to_sym
-293:           end
-294:         when REGEX_LIST
-295:           option.on( "-#{cast[:short]}", "--#{cast[:long]} A", Array) do |a|
-296:             @options[cast[:long]] = a
-297:           end
-298:         when REGEX_INT
-299:           option.on("-#{cast[:short]}", "--#{cast[:long]} I", Integer) do |i|
-300:             @options[cast[:long]] = i
-301:           end
-302:         when REGEX_STRING
-303:           option.on("-#{cast[:short]}", "--#{cast[:long]} S", String) do |s|
-304:             @options[cast[:long]] = s
-305:           end
-306:         else
-307:           raise ArgumentError, "Unknown option type: '#{cast[:type]}'"
-308:         end
-309:       end
-310:     end
-311: 
-312:     option_parser.parse!(@argv)
-313: 
-314:     if print_usage_full?
-315:       print_usage_and_exit(true)
-316:     elsif print_usage_short?
-317:       print_usage_and_exit
-318:     end
-319: 
-320:     options_default
-321:     options_glob
-322:     options_check
-323: 
-324:     @options
-325:   end
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- -
- -

-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. -

- - - - - -
- - - - -
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- -
- -

-Check if full “usage info” should be printed. -

- - - -
-
-     # File biopieces.rb, line 335
-335:   def print_usage_full?
-336:     @options[:help]
-337:   end
-
- -
- - - - -
- - -
- - -
- - print_usage_short?() - click to toggle source - -
- -
- -

-Check if short “usage info” should be printed. -

- - - -
-
-     # File biopieces.rb, line 340
-340:   def print_usage_short?
-341:     if not $stdin.tty?
-342:       return false
-343:     elsif @options[:stream_in]
-344:       return false
-345:     elsif @options[:data_in]
-346:       return false
-347:     elsif wiki_path =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/  # TODO get rid of this!
-348:       return false
-349:     else
-350:       return true
-351:     end
-352:   end
-
- -
- - - - -
- - -
- - -
- - wiki_path() - click to toggle source - -
- -
- -

-Given the script name determine the path of the wiki file with the usage -info. -

- - - -
-
-     # File biopieces.rb, line 328
-328:   def wiki_path
-329:     path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
-330:     raise "No such wiki file: #{path}" unless File.file? path
-331:     path
-332:   end
-
- -
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- - - - diff --git a/code_ruby/Maasha/lib/doc/Read.html b/code_ruby/Maasha/lib/doc/Read.html deleted file mode 100644 index 32cd91e..0000000 --- a/code_ruby/Maasha/lib/doc/Read.html +++ /dev/null @@ -1,646 +0,0 @@ - - - - - - - Class: Read - - - - - - - - - - - -
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Read

- -
-

-Class containing data accessor methods for an SFF -entry and methods for manipulating this entry. -

- -
- - - - - - -
-

Attributes

- - -
- - - - -
- read_header_length[RW] -
- -
- - - -
-
- -
- - - - -
- name_length[RW] -
- -
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- -
- - - - -
- number_of_bases[RW] -
- -
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- -
- - - - -
- clip_qual_left[RW] -
- -
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- -
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- -
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- -
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- -
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- flow_index_per_base[RW] -
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- - - - -
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- -
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- quality_scores[RW] -
- -
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- - - - -
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- y_pos[RW] -
- -
- - - -
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Public Instance Methods

- - -
- - -
- - clip() - click to toggle source - -
- -
- -

-Method that clips sequence (i.e. trims) according to clip_qual_left and clip_qual_right information. -

- - - -
-
-     # File sff.rb, line 228
-228:   def clip
-229:     self.bases          = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
-230:     self.quality_scores = self.quality_scores[self.clip_qual_left - 1 ... self.clip_qual_right]
-231:   end
-
- -
- - - - -
- - -
- - -
- - mask() - click to toggle source - -
- -
- -

-Method that soft masks the sequence (i.e. lowercases sequence) according to -clip_qual_left and clip_qual_right information. -

- - - -
-
-     # File sff.rb, line 218
-218:   def mask
-219:     left   = self.bases[0 ... self.clip_qual_left - 1].downcase
-220:     middle = self.bases[self.clip_qual_left - 1 ... self.clip_qual_right]
-221:     right  = self.bases[self.clip_qual_right ... self.bases.length].downcase
-222: 
-223:     self.bases = left + middle + right
-224:   end
-
- -
- - - - -
- - -
- - -
- - to_bp() - click to toggle source - -
- -
- -

-Method that converts a Read object’s data to -a Biopiece record (a hash). -

- - - -
-
-     # File sff.rb, line 197
-197:   def to_bp
-198:     coordinates_get
-199: 
-200:     hash = {}
-201: 
-202:     hash[:SEQ_NAME]           = self.name
-203:     hash[:SEQ]                = self.bases
-204:     hash[:SEQ_LEN]            = self.bases.length
-205:     hash[:CLIP_QUAL_LEFT]     = self.clip_qual_left     - 1
-206:     hash[:CLIP_QUAL_RIGHT]    = self.clip_qual_right    - 1
-207:     hash[:CLIP_ADAPTOR_LEFT]  = self.clip_adapter_left  - 1
-208:     hash[:CLIP_ADAPTOR_RIGHT] = self.clip_adaptor_right - 1
-209:     hash[:SCORES]             = self.quality_scores.map { |i| (i += 64).chr }.join ""
-210:     hash[:X_POS]              = self.x_pos
-211:     hash[:Y_POS]              = self.y_pos
-212: 
-213:     hash
-214:   end
-
- -
- - - - -
- - -
- -
-

Private Instance Methods

- - -
- - -
- - coordinates_get() - click to toggle source - -
- -
- -

-Method that extracts the X/Y coordinates from an SFF -read name encoded with base36. -

- - - -
-
-     # File sff.rb, line 237
-237:   def coordinates_get
-238:     base36 = self.name[5, 5]
-239:     num    = Base36.decode(base36)
-240: 
-241:     self.x_pos = num >> BIT_SHIFT
-242:     self.y_pos = num &  BIT_MASK
-243:   end
-
- -
- - - - -
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- - -
- - -
- -

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- -
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- - - - diff --git a/code_ruby/Maasha/lib/doc/SFF.html b/code_ruby/Maasha/lib/doc/SFF.html deleted file mode 100644 index f3497f6..0000000 --- a/code_ruby/Maasha/lib/doc/SFF.html +++ /dev/null @@ -1,712 +0,0 @@ - - - - - - - Class: SFF - - - - - - - - - - - -
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SFF

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-

-Class containing methods to parse SFF files: www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff -

- -
- - - - - - - - - -
-

Public Class Methods

- - -
- - -
- - new(io) - click to toggle source - -
- -
- -

-Method to initialize an SFF object along with -instance variables pertaining to the SFF header -section. -

- - - -
-
-    # File sff.rb, line 58
-58:   def initialize(io)
-59:     @io                       = io
-60:     @magic_number             = 0
-61:     @version                  = ""
-62:     @index_offset             = 0
-63:     @index_length             = 0
-64:     @number_of_reads          = 0
-65:     @header_length            = 0
-66:     @key_length               = 0
-67:     @number_of_flows_per_read = 0
-68:     @flowgram_format_code     = 0
-69:     @flow_chars               = ""
-70:     @key_sequence             = ""
-71:     @eight_byte_padding       = 0
-72: 
-73:     header_parse
-74:   end
-
- -
- - - - -
- - -
- - -
- - open(*args) - click to toggle source - -
- -
- -

-Class method for opening SFF files. -

- - - -
-
-    # File sff.rb, line 41
-41:   def self.open(*args)
-42:     ios = File.open(*args)
-43: 
-44:     if block_given?
-45:       begin
-46:         yield self.new(ios)
-47:       ensure
-48:         ios.close
-49:       end
-50:     else
-51:       return self.new(ios)
-52:     end
-53:   end
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- -
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Public Instance Methods

- - -
- - -
- - close() - click to toggle source - -
- -
- -

-Method to close ios. -

- - - -
-
-    # File sff.rb, line 77
-77:   def close
-78:     @io.close
-79:   end
-
- -
- - - - -
- - -
- - -
- - each() - click to toggle source - -
- -
- -

-Method to iterate over each SFF entry. -

- - - -
-
-    # File sff.rb, line 82
-82:   def each
-83:     while (read = read_parse) do
-84:       yield read
-85:     end
-86: 
-87:     self   # conventionally
-88:   end
-
- -
- - - - -
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- -
-

Private Instance Methods

- - -
- - -
- - check_header_length() - click to toggle source - -
- -
- -

-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. -

- - - -
-
-     # File sff.rb, line 183
-183:   def check_header_length
-184:     raise SFFError, "Bad header length: #{header_length}" unless @io.pos == @header_length
-185:   end
-
- -
- - - - -
- - -
- - -
- - check_magic_number() - click to toggle source - -
- -
- -

-Method to check the magic number of an SFF file. -Raises an error if the magic number don’t match. -

- - - -
-
-     # File sff.rb, line 170
-170:   def check_magic_number
-171:     raise SFFError, "Badly formatted SFF file." unless @magic_number == 779314790
-172:   end
-
- -
- - - - -
- - -
- - -
- - check_version() - click to toggle source - -
- -
- -

-Method to check the version number of an SFF file. -Raises an error if the version don’t match. -

- - - -
-
-     # File sff.rb, line 176
-176:   def check_version
-177:     raise SFFError, "Wrong version: #{@version}" unless @version.to_i == 1
-178:   end
-
- -
- - - - -
- - -
- - -
- - fast_forward() - click to toggle source - -
- -
- -

-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. -

- - - -
-
-     # File sff.rb, line 122
-122:   def fast_forward
-123:     eight_byte_padding = 8 - (@io.pos % 8)
-124: 
-125:     @io.read(eight_byte_padding) unless eight_byte_padding == 8
-126:   end
-
- -
- - - - -
- - -
- - -
- - header_parse() - click to toggle source - -
- -
- -

-Method to parse the SFF file’s header section -and load the information into the instance variables. -

- - - -
-
-     # File sff.rb, line 94
- 94:   def header_parse
- 95:     template     = "NC4N2NNnnnC"
- 96:     bits_in_uint = 32
- 97: 
- 98:     data = @io.read(31).unpack(template)
- 99:     
-100:     @magic_number             = data[0]
-101:     @version                  = data[1 .. 4].join ""
-102:     @index_offset             = (data[5] << bits_in_uint) | data[6]
-103:     @index_length             = data[7]
-104:     @number_of_reads          = data[8]
-105:     @header_length            = data[9]
-106:     @key_length               = data[10]
-107:     @number_of_flows_per_read = data[11]
-108:     @flowgram_format_code     = data[12]
-109:     @flow_chars               = @io.read(@number_of_flows_per_read).unpack("A*").join ""
-110:     @key_sequence             = @io.read(@key_length).unpack("A*").join ""
-111: 
-112:     fast_forward
-113: 
-114:     check_magic_number
-115:     check_version
-116:     check_header_length
-117:   end
-
- -
- - - - -
- - -
- - -
- - read_parse() - click to toggle source - -
- -
- -

-Method to parse a read section of an SFF file. -

- - - -
-
-     # File sff.rb, line 129
-129:   def read_parse
-130:     return nil if @number_of_reads == @@count
-131: 
-132:     template = "nnNnnnn"
-133: 
-134:     read = Read.new()
-135: 
-136:     data = @io.read(16).unpack(template)
-137: 
-138:     read.read_header_length  = data[0]
-139:     read.name_length         = data[1]
-140:     read.number_of_bases     = data[2]
-141:     read.clip_qual_left      = data[3]
-142:     read.clip_qual_right     = data[4]
-143:     read.clip_adapter_left   = data[5]
-144:     read.clip_adaptor_right  = data[6]
-145:     read.name                = @io.read(read.name_length).unpack("A*").join ""
-146: 
-147:     fast_forward
-148: 
-149:     @io.read(2 * @number_of_flows_per_read) # skip through flowgram_values
-150:     @io.read(read.number_of_bases)          # skip through flow_index_per_base
-151: 
-152:     # NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.
-153:     # read.flowgram_values     = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }
-154:     # flow_index_per_base      = @io.read(read.number_of_bases).unpack("C*")
-155:     # (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }
-156:     # read.flow_index_per_base = flow_index_per_base
-157: 
-158:     read.bases               = @io.read(read.number_of_bases).unpack("A*").join ""
-159:     read.quality_scores      = @io.read(read.number_of_bases).unpack("C*")
-160: 
-161:     fast_forward
-162: 
-163:     @@count += 1
-164: 
-165:     read
-166:   end
-
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-Error class for all exceptions to do with SFF. -

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- - - - diff --git a/code_ruby/Maasha/lib/doc/Seq.html b/code_ruby/Maasha/lib/doc/Seq.html deleted file mode 100644 index b458f01..0000000 --- a/code_ruby/Maasha/lib/doc/Seq.html +++ /dev/null @@ -1,1825 +0,0 @@ - - - - - - - Class: Seq - - - - - - - - - - - -
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Seq

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Attributes

- - -
- - - - -
- seq_name[RW] -
- -
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- -
- - - - -
- seq[RW] -
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- - - - -
- type[RW] -
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- qual[RW] -
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-

Public Class Methods

- - -
- - -
- - generate_oligos(length, type) - click to toggle source - -
- -
- -

-Method that generates all possible oligos of a specifed length and type. -

- - - -
-
-    # File seq.rb, line 47
-47:   def self.generate_oligos(length, type)
-48:     raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
-49: 
-50:     case type.downcase
-51:     when /dna/     then alph = DNA
-52:     when /rna/     then alph = RNA
-53:     when /protein/ then alph = PROTEIN
-54:     else
-55:       raise SeqError, "Unknown sequence type: #{type}"
-56:     end
-57: 
-58:     oligos = [""]
-59: 
-60:     (1 .. length).each do
-61:       list = []
-62: 
-63:       oligos.each do |oligo|
-64:         alph.each do |char|
-65:           list << oligo + char
-66:         end
-67:       end
-68: 
-69:       oligos = list
-70:     end
-71: 
-72:     oligos
-73:   end
-
- -
- - - - -
- - -
- - -
- - new(seq_name = nil, seq = nil, type = nil, qual = nil) - click to toggle source - -
- -
- -

-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. -

    -
    • -
- - - -
-
-    # File seq.rb, line 80
-80:   def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
-81:     @seq_name = seq_name
-82:     @seq      = seq
-83:     @type     = type
-84:     @qual     = qual
-85:   end
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- -
- - - - -
- - -
- -
-

Public Instance Methods

- - -
- - -
- - adaptor_clip_left(adaptor, hd_percent = 0) - click to toggle source - -
- -
- -

-Method that locates an adaptor or part thereof in the sequence of a Seq 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. -

- - - -
-
-     # File seq.rb, line 377
-377:   def adaptor_clip_left(adaptor, hd_percent = 0)
-378:     pos = self.adaptor_locate_left(adaptor, hd_percent)
-379: 
-380:     if pos > 0
-381:       self.seq  = self.seq[pos + 1 ... self.length]
-382:       self.qual = self.qual[pos + 1 ... self.qual.length] unless self.qual.nil?
-383:     end
-384:   end
-
- -
- - - - -
- - -
- - -
- - adaptor_clip_right(adaptor, hd_percent = 0) - click to toggle source - -
- -
- -

-Method that locates an adaptor or part thereof in the sequence of a Seq 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. -

- - - -
-
-     # File seq.rb, line 364
-364:   def adaptor_clip_right(adaptor, hd_percent = 0)
-365:     pos = self.adaptor_locate_right(adaptor, hd_percent)
-366: 
-367:     if pos > 0
-368:       self.seq  = self.seq[0 ... pos]
-369:       self.qual = self.qual[0 ... pos] unless self.qual.nil?
-370:     end
-371:   end
-
- -
- - - - -
- - -
- - -
- - adaptor_locate_left(adaptor, hd_percent = 0) - click to toggle source - -
- -
- -

-Method that locates an adaptor or part thereof in the sequence of a Seq 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. -

- - - -
-
-     # File seq.rb, line 340
-340:   def adaptor_locate_left(adaptor, hd_percent = 0)
-341:     raise SeqError, "Hamming distance percent out of range #{hd_percent}" unless (0 .. 100).include? hd_percent
-342:     pos = adaptor.length
-343: 
-344:     while pos > 0
-345:       len          = pos
-346:       subseq       = self.seq[0 ... len].upcase
-347:       subadaptor   = adaptor[adaptor.length - len ... adaptor.length].upcase
-348:       m            = Hamming.new(subseq)
-349:       hamming_dist = m.match(subadaptor)
-350:       hamming_max  = (len * hd_percent * 0.01).round
-351: 
-352:       pos -= 1
-353: 
-354:       return pos if hamming_dist <= hamming_max
-355:     end
-356:     
-357:     1
-358:   end
-
- -
- - - - -
- - -
- - -
- - adaptor_locate_right(adaptor, hd_percent = 0) - click to toggle source - -
- -
- -

-Method that locates an adaptor or part thereof in the sequence of a Seq 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. -

- - - -
-
-     # File seq.rb, line 316
-316:   def adaptor_locate_right(adaptor, hd_percent = 0)
-317:     raise SeqError, "Hamming distance percent out of range #{hd_percent}" unless (0 .. 100).include? hd_percent
-318:     pos = self.length - adaptor.length
-319: 
-320:     while pos < self.length
-321:       len          = self.length - pos
-322:       subseq       = self.seq[pos ... pos + len].upcase
-323:       subadaptor   = adaptor[0 ... len].upcase
-324:       m            = Hamming.new(subseq)
-325:       hamming_dist = m.match(subadaptor)
-326:       hamming_max  = (len * hd_percent * 0.01).round
-327:       return pos if hamming_dist <= hamming_max
-328: 
-329:       pos += 1
-330:     end
-331: 
-332:     1
-333:   end
-
- -
- - - - -
- - -
- - -
- - complement() - click to toggle source - -
- -
- -

-Method that complements sequence including ambiguity codes. -

- - - -
-
-     # File seq.rb, line 196
-196:   def complement
-197:     raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
-198: 
-199:     if self.is_dna?
-200:       self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
-201:     elsif self.is_rna?
-202:       self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
-203:     else
-204:       raise SeqError, "Cannot complement sequence type: #{self.type}"
-205:     end
-206:   end
-
- -
- - - - -
- - -
- - -
- - composition() - click to toggle source - -
- -
- -

-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. -

- - - -
-
-     # File seq.rb, line 272
-272:   def composition
-273:     comp = Hash.new(0);
-274: 
-275:     self.seq.upcase.each_char do |char|
-276:       comp[char] += 1
-277:     end
-278: 
-279:     comp
-280:   end
-
- -
- - - - -
- - -
- - -
- - convert_phred2illumina!() - click to toggle source - -
- -
- -

-Method to convert the quality scores from a specified base to another base. -

- - - -
-
-     # File seq.rb, line 388
-388:   def convert_phred2illumina!
-389:     self.qual.gsub! /./ do |score|
-390:       score_phred  = score.ord - SCORE_PHRED
-391:       raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred
-392:       score_illumina = score_phred + SCORE_ILLUMINA
-393:       score          = score_illumina.chr
-394:     end
-395:   end
-
- -
- - - - -
- - -
- - -
- - convert_solexa2illumina!() - click to toggle source - -
- -
- -

-Method to convert the quality scores from Solexa odd/ratio to Illumina -format. -

- - - -
-
-     # File seq.rb, line 399
-399:   def convert_solexa2illumina!
-400:     self.qual.gsub! /./ do |score|
-401:       score = solexa_char2illumina_char(score)
-402:     end
-403:   end
-
- -
- - - - -
- - -
- - -
- - generate(length, type) - click to toggle source - -
- -
- -

-Method that generates a random sequence of a given length and type. -

- - - -
-
-     # File seq.rb, line 209
-209:   def generate(length, type)
-210:     raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
-211: 
-212:     case type.downcase
-213:     when "dna"
-214:       alph = DNA
-215:     when "rna"
-216:       alph = RNA
-217:     when "protein"
-218:       alph = PROTEIN
-219:     else
-220:       raise SeqError, "Unknown sequence type: #{type}"
-221:     end
-222: 
-223:     seq_new   = Array.new(length) { alph[rand(alph.size)] }.join("")
-224:     self.seq  = seq_new
-225:     self.type = type.downcase
-226:     seq_new
-227:   end
-
- -
- - - - -
- - -
- - -
- - hard_mask() - click to toggle source - -
- -
- -

-Method that returns the percentage of hard masked residues or N’s in -a sequence. -

- - - -
-
-     # File seq.rb, line 301
-301:   def hard_mask
-302:     ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
-303:   end
-
- -
- - - - -
- - -
- - -
- - homopol_max(min = 1) - click to toggle source - -
- -
- -

-Method that returns the length of the longest homopolymeric stretch found -in a sequence. -

- - - -
-
-     # File seq.rb, line 284
-284:   def homopol_max(min = 1)
-285:     return 0 if self.seq.nil? or self.seq.empty?
-286: 
-287:     found = false
-288: 
-289:     self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
-290:       found = true
-291:       min   = match.size > min ? match.size : min
-292:     end
-293: 
-294:     return 0 unless found
-295:  
-296:     min
-297:   end
-
- -
- - - - -
- - -
- - -
- - indels() - click to toggle source - -
- -
- -

-Return the number indels in a sequence. -

- - - -
-
-    # File seq.rb, line 95
-95:   def indels
-96:     regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
-97:     self.seq.scan(regex).size
-98:   end
-
- -
- - - - -
- - -
- - -
- - is_dna?() - click to toggle source - -
- -
- -

-Method that returns true is a given sequence type is DNA. -

- - - -
-
-     # File seq.rb, line 101
-101:   def is_dna?
-102:     self.type == 'dna'
-103:   end
-
- -
- - - - -
- - -
- - -
- - is_protein?() - click to toggle source - -
- -
- -

-Method that returns true is a given sequence type is protein. -

- - - -
-
-     # File seq.rb, line 111
-111:   def is_protein?
-112:     self.type == 'protein'
-113:   end
-
- -
- - - - -
- - -
- - -
- - is_rna?() - click to toggle source - -
- -
- -

-Method that returns true is a given sequence type is RNA. -

- - - -
-
-     # File seq.rb, line 106
-106:   def is_rna?
-107:     self.type == 'rna'
-108:   end
-
- -
- - - - -
- - -
- - -
- - len() - click to toggle source - -
- -
- - - - - -
- - - - -
- Alias for: length -
- -
- - -
- - -
- - length() - click to toggle source - -
- -
- -

-Returns the length of a sequence. -

- - - -
-
-    # File seq.rb, line 88
-88:   def length
-89:     self.seq.nil? ? 0 : self.seq.length
-90:   end
-
- -
- - -
- Also aliased as: len -
- - - -
- - -
- - -
- - match(patter, pos) - click to toggle source - -
- -
- - 
-  seq.match(pattern[, pos ] [, hd=max] [, ed=max]) -> matchdata or nil
-
-

-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. -

- - - -
-
-     # File seq.rb, line 411
-411:   def match(patter, pos)
-412:   end
-
- -
- - - - -
- - -
- - -
- - revcomp() - click to toggle source - -
- -
- - - - - -
- - - - -
- Alias for: reverse_complement -
- -
- - -
- - -
- - reverse() - click to toggle source - -
- -
- -

-Method to reverse the sequence. -

- - - -
-
-     # File seq.rb, line 191
-191:   def reverse
-192:     self.seq.reverse!
-193:   end
-
- -
- - - - -
- - -
- - -
- - reverse_complement() - click to toggle source - -
- -
- -

-Method to reverse complement sequence. -

- - - -
-
-     # File seq.rb, line 183
-183:   def reverse_complement
-184:     self.reverse
-185:     self.complement
-186:   end
-
- -
- - -
- Also aliased as: revcomp -
- - - -
- - -
- - -
- - soft_mask() - click to toggle source - -
- -
- -

-Method that returns the percentage of soft masked residues or lower cased -residues in a sequence. -

- - - -
-
-     # File seq.rb, line 307
-307:   def soft_mask
-308:     ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
-309:   end
-
- -
- - - - -
- - -
- - -
- - subseq(start, length = self.length - start) - click to toggle source - -
- -
- -

-Method that returns a subsequence of from a given start position and of a -given length. -

- - - -
-
-     # File seq.rb, line 231
-231:   def subseq(start, length = self.length - start)
-232:     raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
-233:     raise SeqError, "subsequence length: #{length} < 1"                                              if length <= 0
-234:     raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-235: 
-236:     stop = start + length - 1
-237: 
-238:     seq  = self.seq[start .. stop]
-239:     qual = self.qual[start .. stop] unless self.qual.nil?
-240: 
-241:     Seq.new(self.seq_name, seq, self.type, qual)
-242:   end
-
- -
- - - - -
- - -
- - -
- - subseq!(start, length = self.length - start) - click to toggle source - -
- -
- -

-Method that replaces a sequence with a subsequence from a given start -position and of a given length. -

- - - -
-
-     # File seq.rb, line 246
-246:   def subseq!(start, length = self.length - start)
-247:     raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
-248:     raise SeqError, "subsequence length: #{length} < 1"                                              if length <= 0
-249:     raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-250: 
-251:     stop = start + length - 1
-252: 
-253:     self.seq  = self.seq[start .. stop]
-254:     self.qual = self.qual[start .. stop] unless self.qual.nil?
-255:   end
-
- -
- - - - -
- - -
- - -
- - subseq_rand(length) - click to toggle source - -
- -
- -

-Method that returns a subsequence of a given length beginning at a random -position. -

- - - -
-
-     # File seq.rb, line 259
-259:   def subseq_rand(length)
-260:     if self.length - length + 1 == 0
-261:       start = 0
-262:     else
-263:       start = rand(self.length - length + 1)
-264:     end
-265: 
-266:     self.subseq(start, length)
-267:   end
-
- -
- - - - -
- - -
- - -
- - to_bp() - click to toggle source - -
- -
- -

-Method that given a Seq entry returns a Biopieces record (a hash). -

- - - -
-
-     # File seq.rb, line 132
-132:   def to_bp
-133:     raise SeqError, "Missing seq_name" if self.seq_name.nil?
-134:     raise SeqError, "Missing seq"      if self.seq.nil?
-135:     record             = {}
-136:     record[:SEQ_NAME] = self.seq_name
-137:     record[:SEQ]      = self.seq
-138:     record[:SEQ_LEN]  = self.length
-139:     record[:SCORES]   = self.qual if self.qual
-140:     record
-141:   end
-
- -
- - - - -
- - -
- - -
- - to_dna() - click to toggle source - -
- -
- -

-Method to reverse-transcribe RNA to DNA. -

- - - -
-
-     # File seq.rb, line 124
-124:   def to_dna
-125:     raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
-126:     raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
-127:     self.type = 'dna'
-128:     self.seq.tr!('Uu','Tt')
-129:   end
-
- -
- - - - -
- - -
- - -
- - to_fasta(wrap = nil) - click to toggle source - -
- -
- -

-Method that given a Seq entry returns a FASTA entry -(a string). -

- - - -
-
-     # File seq.rb, line 144
-144:   def to_fasta(wrap = nil)
-145:     raise SeqError, "Missing seq_name" if self.seq_name.nil?
-146:     raise SeqError, "Missing seq"      if self.seq.nil?
-147: 
-148:     seq_name = self.seq_name
-149:     seq      = self.seq
-150: 
-151:     unless wrap.nil?
-152:       seq.gsub! /(.{#{wrap}})/ do |match|
-153:         match << "\n"
-154:       end
-155: 
-156:       seq.chomp!
-157:     end
-158: 
-159:     ">#{seq_name}\n#{seq}\n"
-160:   end
-
- -
- - - - -
- - -
- - -
- - to_key() - click to toggle source - -
- -
- -

-Method that generates a unique key for a DNA sequence and return this key -as a Fixnum. -

- - - -
-
-     # File seq.rb, line 164
-164:   def to_key
-165:     key = 0
-166:     
-167:     self.seq.upcase.each_char do |char|
-168:       key <<= 2
-169:       
-170:       case char
-171:       when 'A' then key |= 0
-172:       when 'C' then key |= 1
-173:       when 'G' then key |= 2
-174:       when 'T' then key |= 3
-175:       else raise SeqError, "Bad residue: #{char}"
-176:       end
-177:     end
-178:     
-179:     key
-180:   end
-
- -
- - - - -
- - -
- - -
- - to_rna() - click to toggle source - -
- -
- -

-Method to transcribe DNA to RNA. -

- - - -
-
-     # File seq.rb, line 116
-116:   def to_rna
-117:     raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
-118:     raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
-119:     self.type = 'rna'
-120:     self.seq.tr!('Tt','Uu')
-121:   end
-
- -
- - - - -
- - -
- -
-

Private Instance Methods

- - -
- - -
- - solexa2phred(score) - click to toggle source - -
- -
- -

-Method to convert a Solexa score (odd ratio) to a phred (probability) -integer score. -

- - - -
-
-     # File seq.rb, line 418
-418:   def solexa2phred(score)
-419:     (10.0 * Math.log(10.0 ** (score / 10.0) + 1.0, 10)).to_i
-420:   end
-
- -
- - - - -
- - -
- - -
- - solexa_char2illumina_char(char) - click to toggle source - -
- -
- -

-Method to convert a Solexa score encoded using base 64 ASCII to a Phred -score encoded using base 64 ASCII. -

- - - -
-
-     # File seq.rb, line 424
-424:   def solexa_char2illumina_char(char)
-425:     score_solexa = char.ord - 64
-426:     score_phred  = solexa2phred(score_solexa)
-427:     (score_phred + 64).chr
-428:   end
-
- -
- - - - -
- - -
- - -
- - -
- -

Disabled; run with --debug to generate this.

- -
- -
-

[Validate]

-

Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/SeqError.html b/code_ruby/Maasha/lib/doc/SeqError.html deleted file mode 100644 index 16dca69..0000000 --- a/code_ruby/Maasha/lib/doc/SeqError.html +++ /dev/null @@ -1,200 +0,0 @@ - - - - - - - Class: SeqError - - - - - - - - - - - -
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SeqError

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-Error class for all exceptions to do with Seq. -

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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/Status.html b/code_ruby/Maasha/lib/doc/Status.html deleted file mode 100644 index a06e728..0000000 --- a/code_ruby/Maasha/lib/doc/Status.html +++ /dev/null @@ -1,524 +0,0 @@ - - - - - - - Class: Status - - - - - - - - - - - -
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Status

- -
-

-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. -

- -
- - - - - - - - - -
-

Public Instance Methods

- - -
- - -
- - delete() - click to toggle source - -
- -
- -

-Delete status file. -

- - - -
-
-     # File biopieces.rb, line 547
-547:   def delete
-548:     File.delete(path)
-549:   end
-
- -
- - - - -
- - -
- - -
- - get_tmpdir() - click to toggle source - -
- -
- -

-Extract the temporary directory path from the status file, and return this -or nil if not found. -

- - - -
-
-     # File biopieces.rb, line 520
-520:   def get_tmpdir
-521:     File.open(path, mode="r") do |fh|
-522:       tmpdir_path = fh.read.chomp.split(";").last
-523:       return tmpdir_path if File.directory?(tmpdir_path)
-524:     end
-525: 
-526:     nil
-527:   end
-
- -
- - - - -
- - -
- - -
- - log(exit_status) - click to toggle source - -
- -
- -

-Write the Biopiece status to the log file. -

- - - -
-
-     # File biopieces.rb, line 530
-530:   def log(exit_status)
-531:     time1   = Time.new.strftime("%Y-%m-%d %X")
-532:     user    = ENV["USER"]
-533:     script  = File.basename($0)
-534: 
-535:     stream = File.open(path)
-536:     time0, args, tmp_dir = stream.first.split(";")
-537:     stream.close
-538: 
-539:     elap     = time_diff(time0, time1)
-540:     command  = [script, args].join(" ") 
-541:     log_file = ENV["BP_LOG"] + "/biopieces.log"
-542: 
-543:     File.open(log_file, mode = "a") { |file| file.puts [time0, time1, elap, user, exit_status, command].join("\t") }
-544:   end
-
- -
- - - - -
- - -
- - -
- - set() - click to toggle source - -
- -
- -

-Write the status to a status file. -

- - - -
-
-     # File biopieces.rb, line 495
-495:   def set
-496:     time0  = Time.new.strftime("%Y-%m-%d %X")
-497: 
-498:     File.open(path, mode="w") do |fh|
-499:       fh.puts [time0, ARGV.join(" ")].join(";")
-500:     end
-501:   end
-
- -
- - - - -
- - -
- - -
- - set_tmpdir(tmpdir_path) - click to toggle source - -
- -
- -

-Append the a temporary directory path to the status file. -

- - - -
-
-     # File biopieces.rb, line 504
-504:   def set_tmpdir(tmpdir_path)
-505:     status = ""
-506: 
-507:     File.open(path, mode="r") do |fh|
-508:       status = fh.read.chomp
-509:     end
-510: 
-511:     status = "#{status};#{tmpdir_path}\n"
-512: 
-513:     File.open(path, mode="w") do |fh|
-514:       fh << status
-515:     end
-516:   end
-
- -
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Private Instance Methods

- - -
- - -
- - path() - click to toggle source - -
- -
- -

-Path to status file -

- - - -
-
-     # File biopieces.rb, line 554
-554:   def path
-555:     user   = ENV["USER"]
-556:     script = File.basename($0)
-557:     pid    = $$
-558:     path   = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
-559:   end
-
- -
- - - - -
- - -
- - -
- - time_diff(t0, t1) - click to toggle source - -
- -
- -

-Get the elapsed time from the difference between two time stamps. -

- - - -
-
-     # File biopieces.rb, line 562
-562:   def time_diff(t0, t1)
-563:     Time.at((DateTime.parse(t1).to_time - DateTime.parse(t0).to_time).to_i).gmtime.strftime('%X')
-564:   end
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[Validate]

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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/Stream.html b/code_ruby/Maasha/lib/doc/Stream.html deleted file mode 100644 index 24d3772..0000000 --- a/code_ruby/Maasha/lib/doc/Stream.html +++ /dev/null @@ -1,557 +0,0 @@ - - - - - - - Class: Stream - - - - - - - - - - - -
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Stream

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Public Class Methods

- - -
- - -
- - open(options, mode, stdio) - click to toggle source - -
- -
- -

-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]. -

- - - -
-
-     # File biopieces.rb, line 572
-572:   def self.open(options, mode, stdio)
-573:     if mode == "r"
-574:       if options[:data_in] and options[:data_in].first == "-"
-575:         self.nread(["-"])
-576:       else
-577:         $stdin.tty? ? read(options[:stream_in]) : stdio
-578:       end
-579:     elsif mode == "w"
-580:       options[:stream_out] ? self.write(options[:stream_out], options[:compress]) : stdio
-581:     else
-582:       raise "Bad mode #{mode}"
-583:     end
-584:   end
-
- -
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Private Class Methods

- - -
- - -
- - nread(files) - click to toggle source - -
- -
- -

-Opens a list of files for reading and return an io object. -

- - - -
-
-     # File biopieces.rb, line 616
-616:   def self.nread(files)
-617:     stdin, stdout, stderr = Open3.popen3("cat " + files.join(' '));
-618:     stdin.close
-619:     stderr.close
-620:     stdout
-621:   end
-
- -
- - - - -
- - -
- - -
- - nwrite(file) - click to toggle source - -
- -
- -

-Opens a file for writing and return an io object. -

- - - -
-
-     # File biopieces.rb, line 624
-624:   def self.nwrite(file)
-625:     File.open(file, mode="w")
-626:   end
-
- -
- - - - -
- - -
- - -
- - read(files) - click to toggle source - -
- -
- -

-Opens a reads stream to a list of files. -

- - - -
-
-     # File biopieces.rb, line 589
-589:   def self.read(files)
-590:     return if files.nil? #TODO case/when
-591:     self.zipped?(files) ? self.zread(files) : self.nread(files)
-592:   end
-
- -
- - - - -
- - -
- - -
- - write(file, zip=nil) - click to toggle source - -
- -
- -

-Opens a write stream to a file and returns a io object. -

- - - -
-
-     # File biopieces.rb, line 595
-595:   def self.write(file, zip=nil)
-596:     zip ? self.zwrite(file) : self.nwrite(file)
-597:   end
-
- -
- - - - -
- - -
- - -
- - zipped?(files) - click to toggle source - -
- -
- -

-Test if a list of files are gzipped or not. Raises if files are mixed -zipped and unzipped. -

- - - -
-
-     # File biopieces.rb, line 630
-630:   def self.zipped?(files)
-631:     type_hash = {}
-632: 
-633:     files.each do |file|
-634:       type = `file #{file}`
-635: 
-636:       if type =~ /gzip compressed/
-637:         type_hash[:gzip] = true
-638:       else
-639:         type_hash[:ascii] = true
-640:       end
-641:     end
-642: 
-643:     raise "Mixture of zipped and unzipped files" if type_hash.size == 2
-644: 
-645:     type_hash[:gzip]
-646:   end
-
- -
- - - - -
- - -
- - -
- - zread(files) - click to toggle source - -
- -
- -

-Opens a list of gzipped files for reading and return an io object. -

- - - -
-
-     # File biopieces.rb, line 600
-600:   def self.zread(files)
-601:     stdin, stdout, stderr = Open3.popen3("zcat " + files.join(' '));
-602:     stdin.close
-603:     stderr.close
-604:     stdout
-605:   end
-
- -
- - - - -
- - -
- - -
- - zwrite(file) - click to toggle source - -
- -
- -

-Opens a file for gzipped writing and return an io object. -

- - - -
-
-     # File biopieces.rb, line 608
-608:   def self.zwrite(file)
-609:     stdin, stdout, stderr = Open3.popen3("gzip -f > #{file}")
-610:     stderr.close
-611:     stdout.close
-612:     stdin
-613:   end
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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/String.html b/code_ruby/Maasha/lib/doc/String.html deleted file mode 100644 index 61c0653..0000000 --- a/code_ruby/Maasha/lib/doc/String.html +++ /dev/null @@ -1,408 +0,0 @@ - - - - - - - Class: String - - - - - - - - - - - -
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String

- -
-

-Monkey patching Class String to add bitwise -operators. Behaviour matching Perl’s: perldoc.perl.org/perlop.html#Bitwise-String-Operators -

- -
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Public Class Methods

- - -
- - -
- - hamming_dist(str1, str2) - click to toggle source - -
- -
- -

-Method to that returns the case senstive Hamming Distance between two -strings. en.wikipedia.org/wiki/Hamming_distance -

- - - -
-
-    # File bits.rb, line 34
-34:   def self.hamming_dist(str1, str2)
-35:     raise StringError, "Uneven string lengths: #{str1.length} != #{str2.length}" if str1.length != str2.length
-36:     (str1 ^ str2 ).count("\x01-\xff")
-37:   end
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- - -
- - -
- - &(str) - click to toggle source - -
- -
- -

-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. -

- - - -
-
-    # File bits.rb, line 43
-43:   def &(str)
-44:     new = ""
-45: 
-46:     (0 ... [self.length, str.length].min).each do |i|
-47:       new << (self[i].ord & str[i].ord)
-48:     end
-49: 
-50:     new
-51:   end
-
- -
- - - - -
- - -
- - -
- - ^(str) - click to toggle source - -
- -
- -

-Method that performs bitwise XOR operation where bits are copied if they -exists in ONE BUT NOT BOTH operands. -

- - - -
-
-    # File bits.rb, line 77
-77:   def ^(str)
-78:     new = ""
-79: 
-80:     (0 ... [self.length, str.length].min).each do |i|
-81:       new << (self[i].ord ^ str[i].ord)
-82:     end
-83: 
-84:     new
-85:   end
-
- -
- - - - -
- - -
- - -
- - |(str) - click to toggle source - -
- -
- -

-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. -

- - - -
-
-    # File bits.rb, line 57
-57:   def |(str)
-58:     new = ""
-59: 
-60:     min = [self.length, str.length].min
-61: 
-62:     (0 ... min).each do |i|
-63:       new << (self[i].ord | str[i].ord)
-64:     end
-65: 
-66:     if self.length > str.length
-67:       new << self[min ... self.length]
-68:     elsif self.length < str.length
-69:       new << str[min ... str.length]
-70:     end
-71: 
-72:     new
-73:   end
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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/StringError.html b/code_ruby/Maasha/lib/doc/StringError.html deleted file mode 100644 index 2151699..0000000 --- a/code_ruby/Maasha/lib/doc/StringError.html +++ /dev/null @@ -1,200 +0,0 @@ - - - - - - - Class: StringError - - - - - - - - - - - -
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StringError

- -
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-Error class for all exceptions to do with String. -

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Disabled; run with --debug to generate this.

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Generated with the Darkfish - Rdoc Generator 1.1.6.

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- - - - diff --git a/code_ruby/Maasha/lib/doc/base36_rb.html b/code_ruby/Maasha/lib/doc/base36_rb.html deleted file mode 100644 index 5b15245..0000000 --- a/code_ruby/Maasha/lib/doc/base36_rb.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - File: base36.rb [RDoc Documentation] - - - - - - - - - - -
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Description

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-Copyright (C) 2011 Martin A. Hansen. -

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- - - diff --git a/code_ruby/Maasha/lib/doc/biopieces_rb.html b/code_ruby/Maasha/lib/doc/biopieces_rb.html deleted file mode 100644 index 9757f4c..0000000 --- a/code_ruby/Maasha/lib/doc/biopieces_rb.html +++ /dev/null @@ -1,62 +0,0 @@ - - - - - - - - File: biopieces.rb [RDoc Documentation] - - - - - - - - - - -
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Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/bits_rb.html b/code_ruby/Maasha/lib/doc/bits_rb.html deleted file mode 100644 index 2380506..0000000 --- a/code_ruby/Maasha/lib/doc/bits_rb.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - File: bits.rb [RDoc Documentation] - - - - - - - - - - -
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-Copyright (C) 2007-2011 Martin A. Hansen. -

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Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.html deleted file mode 100644 index b5ad0f7..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.html +++ /dev/null @@ -1,301 +0,0 @@ - - - - Class: Biopieces [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassBiopieces
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - Object - -
-
- - -
- -
- -
-

-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 seperated by a colon and a white -space ’: ’. Each record is separated by a line with three -dashes ’—’. -

- -
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Methods

- -
- - each   - - each_record   - - mktmpdir   - - new   - - parse   - - puts   - -
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- - -
- - -
- - - - new(test=nil, input=STDIN, output=STDOUT) - - - -
- -
- -

-Initialize a Biopiece and write the status to file. Options are for testing -purposes only. -

- -
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Public Instance methods

- - -
- - -
- - each() - -
- -
- -

-Alias for each_record -

- -
-
- - -
- - -
- - - - each_record() {|record unless record.empty?| ...} - - - -
- -
- -

-Open Biopiece input stream if not open and iterate over all Biopiece -records in the stream. -

- -
-
- - -
- - -
- - - - mktmpdir() - - - -
- -
- -

-Create a temporary directory inside the ENV[“BP_TMP“] dir. -

- -
-
- - -
- - -
- - - - parse(argv, cast_list=[], script_path=$0) - - - -
- -
- -

-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. -

- -
-
- - -
- - -
- - - - puts(record) - - - -
- -
- -

-Open Biopiece output stream if not open and puts record to the stream. -

- -
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-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000001.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000001.html deleted file mode 100644 index 7e9371a..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000001.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - new (Biopieces) - - - - - 
# File biopieces.rb, line 43
-  def initialize(test=nil, input=STDIN, output=STDOUT)
-    @test   = test
-    @input  = input
-    @output = output
-    @status = Status.new
-    @status.set unless @test
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000002.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000002.html deleted file mode 100644 index b69e120..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000002.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - parse (Biopieces) - - - - - 
# File biopieces.rb, line 54
-  def parse(argv, cast_list=[], script_path=$0)
-    casts          = Casts.new(cast_list)
-    option_handler = OptionHandler.new(argv, casts, script_path, @test)
-    @options       = option_handler.options_parse
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000003.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000003.html deleted file mode 100644 index 2675d14..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000003.html +++ /dev/null @@ -1,34 +0,0 @@ - - - - each_record (Biopieces) - - - - - 
# File biopieces.rb, line 62
-  def each_record
-    @in = Stream::open(@options, mode="r", @input) unless @in.is_a? IO
-    return if @in.nil?
-
-    record = {}
-
-    @in.each_line do |line|
-      case line
-      when /^([^:]+): (.*)$/
-        record[$1] = $2
-      when /^---$/
-        yield record unless record.empty?
-        record = {}
-      else
-        raise "Bad record format: #{line}"
-      end
-    end
-
-    yield record unless record.empty?
-
-    self # conventionally
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000005.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000005.html deleted file mode 100644 index cb2274b..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000005.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - puts (Biopieces) - - - - - 
# File biopieces.rb, line 88
-  def puts(record)
-    @out = Stream::open(@options, mode="w", @output) unless @out.is_a? IO
-
-    record.each do |key,value|
-      @out.print "#{key}: #{value}\n"
-    end
-
-    @out.print "---\n"
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000006.html b/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000006.html deleted file mode 100644 index 9e4ff5e..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000006.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - mktmpdir (Biopieces) - - - - - 
# File biopieces.rb, line 99
-  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.set_tmpdir(path)
-    path
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/CastError.html b/code_ruby/Maasha/lib/doc/classes/CastError.html deleted file mode 100644 index bec2260..0000000 --- a/code_ruby/Maasha/lib/doc/classes/CastError.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - Class: CastError [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassCastError
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - StandardError - -
-
- - -
- -
- -
-

-Error class for all exceptions to do with option casts. -

- -
- -
- - -
- - - -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Casts.html b/code_ruby/Maasha/lib/doc/classes/Casts.html deleted file mode 100644 index b0a6e48..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Casts.html +++ /dev/null @@ -1,187 +0,0 @@ - - - - Class: Casts [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassCasts
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - Array - -
-
- - -
- -
- -
-

-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. -

- -
- -
- - -
-

Methods

- -
- - new   - -
-
- -
- - - -
- -
-

Constants

- -
- - - - - - - - - - - - - - - - -
TYPES=%w[flag string list int uint float file file! files files! dir dir! genome]
MANDATORY=%w[long short type mandatory default allowed disallowed]
-
-
- - - - - - -
- -

Public Class methods

- - -
- - -
- - - - new(cast_list=[]) - - - -
- -
- -

-Initialize cast object with an optional options cast list to which -ubiquitous casts are added after which all casts are checked. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Casts.src/M000007.html b/code_ruby/Maasha/lib/doc/classes/Casts.src/M000007.html deleted file mode 100644 index 8ae5d3f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Casts.src/M000007.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - new (Casts) - - - - - 
# File biopieces.rb, line 125
-  def initialize(cast_list=[])
-    @cast_list = cast_list
-    ubiquitous
-    check
-    self.push *@cast_list
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Fasta.html b/code_ruby/Maasha/lib/doc/classes/Fasta.html deleted file mode 100644 index ab36f56..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Fasta.html +++ /dev/null @@ -1,266 +0,0 @@ - - - - Class: Fasta [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassFasta
In: - - - - - fasta.rb - - - - -
- -
Parent: - - Object - -
-
- - -
- -
- -
- - -
-

Methods

- -
- - close   - - each   - - get_entry   - - new   - - open   - -
-
- -
- - - -
-

Included Modules

- -
- - Enumerable - -
-
- -
- - - - - - -
- -

Public Class methods

- - -
- - -
- - - - new(io, type=nil) - - - -
- -
- -
-
- - -
- - -
- - - - open(*args) {|ios| ...} - - - -
- -
- -

-Class method allowing open to be used on (zipped) files. See File.open. -

- -
-
- - -

Public Instance methods

- - -
- - -
- - - - close() - - - -
- -
- -

-Method to close ios. -

- -
-
- - -
- - -
- - - - each() {|entry| ...} - - - -
- -
- -

-Iterator method for parsing FASTA enries. -

- -
-
- - -
- - -
- - - - get_entry() - - - -
- -
- -

-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. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000031.html b/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000031.html deleted file mode 100644 index c9a4be0..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000031.html +++ /dev/null @@ -1,28 +0,0 @@ - - - - open (Fasta) - - - - - 
# File fasta.rb, line 33
-  def self.open(*args)
-    ios   = File.open(*args)
-    fasta = self.new(ios)
-
-    if block_given?
-      begin
-        yield fasta
-      ensure
-        ios.close
-      end
-
-      return true
-    else
-      return fasta
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000032.html b/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000032.html deleted file mode 100644 index ad1c045..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000032.html +++ /dev/null @@ -1,16 +0,0 @@ - - - - new (Fasta) - - - - - 
# File fasta.rb, line 50
-  def initialize(io, type=nil)
-    @io   = io
-    @type = type
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000033.html b/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000033.html deleted file mode 100644 index 40d2bc9..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000033.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - each (Fasta) - - - - - 
# File fasta.rb, line 56
-  def each
-    while entry = get_entry do
-      yield entry
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000034.html b/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000034.html deleted file mode 100644 index 62a8104..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Fasta.src/M000034.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - get_entry (Fasta) - - - - - 
# File fasta.rb, line 64
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/FastaError.html b/code_ruby/Maasha/lib/doc/classes/FastaError.html deleted file mode 100644 index d188d55..0000000 --- a/code_ruby/Maasha/lib/doc/classes/FastaError.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - Class: FastaError [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassFastaError
In: - - - - - fasta.rb - - - - -
- -
Parent: - - StandardError - -
-
- - -
- -
- -
-

-Error class for all exceptions to do with FASTA. -

- -
- -
- - -
- - - -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.html deleted file mode 100644 index 177aca6..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.html +++ /dev/null @@ -1,615 +0,0 @@ - - - - Class: OptionHandler [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassOptionHandler
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - Object - -
-
- - -
- -
- -
-

-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. -

- -
- -
- - - - -
- - - -
- -
-

Constants

- -
- - - - - - - - - - - - - - - - - - - - - - - -
REGEX_LIST=/^(list|files|files!)$/
REGEX_INT=/^(int|uint)$/
REGEX_STRING=/^(string|file|file!|dir|dir!|genome)$/
-
-
- - - - - - -
- -

Public Class methods

- - - - - -

Public Instance methods

- - -
- - -
- - - - options_check() - - - -
- -
- -

-Check all options according to casts. -

- -
-
- - -
- - -
- - - - options_check_allowed(cast) - - - -
- -
- -

-Check options and raise unless allowed. -

- -
-
- - -
- - -
- - - - options_check_dir(cast) - - - -
- -
- -

-Check dir! type argument and raise if directory don’t exist. -

- -
-
- - -
- - -
- - - - options_check_disallowed(cast) - - - -
- -
- -

-Check disallowed argument values and raise if disallowed. -

- -
-
- - -
- - -
- - - - options_check_file(cast) - - - -
- -
- -

-Check file! type argument and raise if file don’t exists. -

- -
-
- - -
- - -
- - - - options_check_files(cast) - - - -
- -
- -

-Check files! type argument and raise if files don’t exists. -

- -
-
- - -
- - -
- - - - options_check_int(cast) - - - -
- -
- -

-Check int type option and raise if not an integer. -

- -
-
- - -
- - -
- - - - options_check_mandatory(cast) - - - -
- -
- -

-Check if a mandatory option is set and raise if it isn’t. -

- -
-
- - -
- - -
- - - - options_check_uint(cast) - - - -
- -
- -

-Check uint type option and raise if not an unsinged integer. -

- -
-
- - -
- - -
- - - - options_default() - - - -
- -
- -

-Set default options value from cast unless a value is set. -

- -
-
- - -
- - -
- - - - options_glob() - - - -
- -
- -

-Expands glob expressions to a full list of paths. Examples: -“*.fna” or “foo.fna,*.fna” or -“foo.fna,/bar/*.fna“ -

- -
-
- - -
- - -
- - - - options_parse() - - - -
- -
- -

-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. -

- -
-
- - -
- - -
- - - - print_usage_and_exit(full=nil) - - - -
- -
- -

-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. -

- -
-
- - -
- - -
- - - - print_usage_full?() - - - -
- -
- -

-Check if full “usage info” should be printed. -

- -
-
- - -
- - -
- - - - print_usage_short?() - - - -
- -
- -

-Check if short “usage info” should be printed. -

- -
-
- - -
- - -
- - - - wiki_path() - - - -
- -
- -

-Given the script name determine the path of the wiki file with the usage -info. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000008.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000008.html deleted file mode 100644 index 5a296d0..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000008.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - new (OptionHandler) - - - - - 
# File biopieces.rb, line 250
-  def initialize(argv, casts, script_path, test=nil)
-    @argv        = argv
-    @casts       = casts
-    @script_path = script_path
-    @test        = test
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000009.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000009.html deleted file mode 100644 index 97be195..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000009.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - options_parse (OptionHandler) - - - - - 
# File biopieces.rb, line 260
-  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 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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000010.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000010.html deleted file mode 100644 index f8f6991..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000010.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - wiki_path (OptionHandler) - - - - - 
# File biopieces.rb, line 308
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000011.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000011.html deleted file mode 100644 index fc4110d..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000011.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - print_usage_full? (OptionHandler) - - - - - 
# File biopieces.rb, line 315
-  def print_usage_full?
-    @options["help"]
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000012.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000012.html deleted file mode 100644 index 454bef7..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000012.html +++ /dev/null @@ -1,25 +0,0 @@ - - - - print_usage_short? (OptionHandler) - - - - - 
# File biopieces.rb, line 320
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000013.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000013.html deleted file mode 100644 index 859c8a1..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000013.html +++ /dev/null @@ -1,27 +0,0 @@ - - - - print_usage_and_exit (OptionHandler) - - - - - 
# File biopieces.rb, line 337
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000014.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000014.html deleted file mode 100644 index 6666325..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000014.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - options_default (OptionHandler) - - - - - 
# File biopieces.rb, line 354
-  def options_default
-    @casts.each do |cast|
-      if cast[:default]
-        @options[cast[:long]] = cast[:default] unless @options.has_key? cast[:long]
-      end
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000015.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000015.html deleted file mode 100644 index 44dfb09..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000015.html +++ /dev/null @@ -1,33 +0,0 @@ - - - - options_glob (OptionHandler) - - - - - 
# File biopieces.rb, line 364
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000016.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000016.html deleted file mode 100644 index 59771a2..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000016.html +++ /dev/null @@ -1,24 +0,0 @@ - - - - options_check (OptionHandler) - - - - - 
# File biopieces.rb, line 387
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000017.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000017.html deleted file mode 100644 index f6c78dd..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000017.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - options_check_mandatory (OptionHandler) - - - - - 
# File biopieces.rb, line 401
-  def options_check_mandatory(cast)
-    if cast[:mandatory]
-      raise ArgumentError, "Mandatory argument: --#{cast[:long]}" unless @options.has_key? cast[:long]
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000018.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000018.html deleted file mode 100644 index 91480ab..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000018.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - options_check_int (OptionHandler) - - - - - 
# File biopieces.rb, line 408
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000019.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000019.html deleted file mode 100644 index 2bae214..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000019.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - options_check_uint (OptionHandler) - - - - - 
# File biopieces.rb, line 417
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000020.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000020.html deleted file mode 100644 index c4ad6f1..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000020.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - options_check_file (OptionHandler) - - - - - 
# File biopieces.rb, line 426
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000021.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000021.html deleted file mode 100644 index 12c6e7b..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000021.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - options_check_files (OptionHandler) - - - - - 
# File biopieces.rb, line 433
-  def options_check_files(cast)
-    if cast[:type] == 'files!' and @options.has_key? cast[:long]
-      @options[cast[:long]].each do |path|
-        raise ArgumentError, "No such file: '#{path}'" unless File.file? path
-      end
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000022.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000022.html deleted file mode 100644 index b7399d7..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000022.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - options_check_dir (OptionHandler) - - - - - 
# File biopieces.rb, line 442
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000023.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000023.html deleted file mode 100644 index de6439e..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000023.html +++ /dev/null @@ -1,20 +0,0 @@ - - - - options_check_allowed (OptionHandler) - - - - - 
# File biopieces.rb, line 449
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000024.html b/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000024.html deleted file mode 100644 index 5bbf893..0000000 --- a/code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000024.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - options_check_disallowed (OptionHandler) - - - - - 
# File biopieces.rb, line 459
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.html b/code_ruby/Maasha/lib/doc/classes/Seq.html deleted file mode 100644 index 2617168..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.html +++ /dev/null @@ -1,412 +0,0 @@ - - - - Class: Seq [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeq
In: - - - - - seq.rb - - - - -
- -
Parent: - - Object - -
-
- - -
- -
- -
- - -
-

Methods

- -
- - complement   - - generate   - - is_dna   - - is_protein   - - is_rna   - - len   - - length   - - to_bp   - - to_dna   - - to_rna   - -
-
- -
- - - -
- - - -
-

Attributes

- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
qual [RW] 
seq [RW] 
seq_name [RW] 
type [RW] 
-
-
- - - - -
- -

Public Instance methods

- - -
- - -
- - - - complement() - - - -
- -
- -

-Method that complements sequence including ambiguity codes. -

- -
-
- - -
- - -
- - - - generate(length,type) - - - -
- -
- -

-Method that generates a random sequence of a given length. -

- -
-
- - -
- - -
- - - - is_dna() - - - -
- -
- -

-Method that returns true is a given sequence type is DNA. -

- -
-
- - -
- - -
- - - - is_protein() - - - -
- -
- -
-
- - -
- - -
- - - - is_rna() - - - -
- -
- -
-
- - -
- - -
- - len() - -
- -
- -

-Alias for length -

- -
-
- - -
- - -
- - - - length() - - - -
- -
- -
-
- - -
- - -
- - - - to_bp() - - - -
- -
- -

-Method that given a Seq entry returns a Biopieces record (a hash). -

- -
-
- - -
- - -
- - - - to_dna() - - - -
- -
- -

-Method to reverse-transcribe RNA to DNA. -

- -
-
- - -
- - -
- - - - to_rna() - - - -
- -
- -

-Method to transcribe DNA to RNA. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000001.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000001.html deleted file mode 100644 index 9817e7f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000001.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - length (Seq) - - - - - 
# File seq.rb, line 11
-  def length
-    self.seq.nil? ? 0 : self.seq.length
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000003.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000003.html deleted file mode 100644 index bb35b7f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000003.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_dna (Seq) - - - - - 
# File seq.rb, line 18
-  def is_dna
-    self.type == 'dna'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000004.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000004.html deleted file mode 100644 index 1ab276a..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000004.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_rna (Seq) - - - - - 
# File seq.rb, line 22
-  def is_rna
-    self.type == 'rna'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000005.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000005.html deleted file mode 100644 index 445bd31..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000005.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_protein (Seq) - - - - - 
# File seq.rb, line 26
-  def is_protein
-    self.type == 'protein'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000006.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000006.html deleted file mode 100644 index 0d2143f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000006.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - to_rna (Seq) - - - - - 
# File seq.rb, line 31
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000007.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000007.html deleted file mode 100644 index 84cddb0..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000007.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - to_dna (Seq) - - - - - 
# File seq.rb, line 39
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000008.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000008.html deleted file mode 100644 index cde9366..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000008.html +++ /dev/null @@ -1,23 +0,0 @@ - - - - complement (Seq) - - - - - 
# File seq.rb, line 47
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000009.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000009.html deleted file mode 100644 index fc415c3..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000009.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - generate (Seq) - - - - - 
# File seq.rb, line 60
-  def generate(length,type)
-    raise SeqError, "Cannot generate negative sequence length: #{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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000031.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000031.html deleted file mode 100644 index 1a623c0..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000031.html +++ /dev/null @@ -1,25 +0,0 @@ - - - - guess_type (Seq) - - - - - 
# File seq.rb, line 4
-        def guess_type
-                raise ArgumentError, "No sequence." if self.empty?
-
-                seq_beg = self[ 0, 100 ].upcase
-
-                if seq_beg.count( "FLPQIE" ) > 0
-                        Seq::AA.new( self )
-                elsif seq_beg.count( "U" ) > 0
-                        Seq::NA::RNA.new( self )
-                else
-                        Seq::NA::DNA.new( self )
-                end
-        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000032.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000032.html deleted file mode 100644 index a03cc80..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000032.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - wrap (Seq) - - - - - 
# File seq.rb, line 19
-        def wrap( width = 80, delimit = "\n" )
-                raise ArgumentError, "Cannot wrap sequence to negative width: #{ width }." if width <= 0
-
-                self.delete!( " \t\n\r" )
-                self.gsub( /.{#{ width }}(?!$)/, "\\0#{ delimit }" )
-        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000033.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000033.html deleted file mode 100644 index a6e505c..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000033.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - wrap! (Seq) - - - - - 
# File seq.rb, line 27
-        def wrap!( width = 80, delimit = "\n" )
-                self.replace( self.wrap( width, delimit ) )
-        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000034.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000034.html deleted file mode 100644 index e50a92b..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000034.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - generate (Seq) - - - - - 
# File seq.rb, line 32
-        def generate( length )
-                raise ArgumentError, "Cannot generate negative sequence length: #{ length }." if length <= 0
-
-                alph = self.residues
-                Array.new( length ) { alph[ rand( alph.size ) ] }.join( "" )
-        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000035.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000035.html deleted file mode 100644 index 9817e7f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000035.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - length (Seq) - - - - - 
# File seq.rb, line 11
-  def length
-    self.seq.nil? ? 0 : self.seq.length
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000037.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000037.html deleted file mode 100644 index bb35b7f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000037.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_dna (Seq) - - - - - 
# File seq.rb, line 18
-  def is_dna
-    self.type == 'dna'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000038.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000038.html deleted file mode 100644 index 1ab276a..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000038.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_rna (Seq) - - - - - 
# File seq.rb, line 22
-  def is_rna
-    self.type == 'rna'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000039.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000039.html deleted file mode 100644 index 445bd31..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000039.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - is_protein (Seq) - - - - - 
# File seq.rb, line 26
-  def is_protein
-    self.type == 'protein'
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000040.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000040.html deleted file mode 100644 index 0d2143f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000040.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - to_rna (Seq) - - - - - 
# File seq.rb, line 31
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000041.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000041.html deleted file mode 100644 index 84cddb0..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000041.html +++ /dev/null @@ -1,18 +0,0 @@ - - - - to_dna (Seq) - - - - - 
# File seq.rb, line 39
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000042.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000042.html deleted file mode 100644 index 85e6cb2..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000042.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - to_bp (Seq) - - - - - 
# File seq.rb, line 47
-  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
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000043.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000043.html deleted file mode 100644 index 19a14ca..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000043.html +++ /dev/null @@ -1,23 +0,0 @@ - - - - complement (Seq) - - - - - 
# File seq.rb, line 58
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000044.html b/code_ruby/Maasha/lib/doc/classes/Seq.src/M000044.html deleted file mode 100644 index 7b22124..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq.src/M000044.html +++ /dev/null @@ -1,31 +0,0 @@ - - - - generate (Seq) - - - - - 
# File seq.rb, line 71
-  def generate(length,type)
-    raise SeqError, "Cannot generate negative sequence length: #{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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/AA.html b/code_ruby/Maasha/lib/doc/classes/Seq/AA.html deleted file mode 100644 index 985ba72..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/AA.html +++ /dev/null @@ -1,193 +0,0 @@ - - - - Class: Seq::AA [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeq::AA
In: - - - - - seq.rb - - - - -
- -
Parent: - - - - Seq - - - -
-
- - -
- -
- -
-

-Class containing methods specific for amino acid (AA) -sequences. -

- -
- -
- - -
-

Methods

- -
- - mol_weight   - - residues   - -
-
- -
- - - -
- - - - - - -
- -

Public Instance methods

- - -
- - -
- - - - mol_weight() - - - -
- -
- -

-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: www.expasy.ch/tools/pscale/Molecularweight.html -

- -
-
- - -
- - -
- - - - residues() - - - -
- -
- -

-Method that returns an array of amino acid residues. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000036.html b/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000036.html deleted file mode 100644 index db8e35b..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000036.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - residues (Seq::AA) - - - - - 
# File seq.rb, line 47
-                def residues
-                        %w{ F L S Y C W P H Q R I M T N K V A D E G }
-                end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000037.html b/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000037.html deleted file mode 100644 index 6bf454b..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000037.html +++ /dev/null @@ -1,44 +0,0 @@ - - - - mol_weight (Seq::AA) - - - - - 
# File seq.rb, line 55
-                def mol_weight
-                        raise ArgumentError, "invalid residues found: #{self.delete("#{residues.join( "" )}")}" if self.upcase =~ /[^#{residues.join( "" )}]/
-
-                        mol_weight_aa = {
-                                "A" => 89.000,    # Ala
-                                "R" => 174.000,   # Arg
-                                "N" => 132.000,   # Asn
-                                "D" => 133.000,   # Asp
-                                "C" => 121.000,   # Cys
-                                "Q" => 146.000,   # Gln
-                                "E" => 147.000,   # Glu
-                                "G" => 75.000,    # Gly
-                                "H" => 155.000,   # His
-                                "I" => 131.000,   # Ile
-                                "L" => 131.000,   # Leu
-                                "K" => 146.000,   # Lys
-                                "M" => 149.000,   # Met
-                                "F" => 165.000,   # Phe
-                                "P" => 115.000,   # Pro
-                                "S" => 105.000,   # Ser
-                                "T" => 119.000,   # Thr
-                                "W" => 204.000,   # Trp
-                                "Y" => 181.000,   # Tyr
-                                "V" => 117.000,   # Val
-                        }
-
-                        mw = 0.0
-
-                        self.upcase.each_char { |c| mw += mol_weight_aa[ c ] }
-
-                        mw
-                end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA.html deleted file mode 100644 index 97c8ec4..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA.html +++ /dev/null @@ -1,130 +0,0 @@ - - - - Class: Seq::NA [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeq::NA
In: - - - - - seq.rb - - - - -
- -
Parent: - - - - Seq - - - -
-
- - -
- -
- -
-

-Class containing methods specific for nucleic acid (NA) sequences. -

- -
- -
- - -
- - - -
- -
-

Classes and Modules

- - Class Seq::NA::DNA
-Class Seq::NA::RNA
- -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.html deleted file mode 100644 index 778adf2..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.html +++ /dev/null @@ -1,217 +0,0 @@ - - - - Class: Seq::NA::DNA [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeq::NA::DNA
In: - - - - - seq.rb - - - - -
- -
Parent: - - - - Seq::NA - - - -
-
- - -
- -
- -
-

-Class containing methods specific for DNA sequences. -

- -
- -
- - -
-

Methods

- -
- - complement   - - residues   - - to_RNA   - -
-
- -
- - - -
- - - - - - -
- -

Public Instance methods

- - -
- - -
- - - - complement() - - - -
- -
- -

-Method that complements DNA sequence including -ambiguity codes. -

- -
-
- - -
- - -
- - - - residues() - - - -
- -
- -

-Method that returns an array of DNA residues. -

- -
-
- - -
- - -
- - - - to_RNA() - - - -
- -
- -

-Method to transcribe DNA to RNA. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000038.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000038.html deleted file mode 100644 index cf7df44..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000038.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - residues (Seq::NA::DNA) - - - - - 
# File seq.rb, line 94
-                        def residues
-                                %w{ A T C G }
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000039.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000039.html deleted file mode 100644 index 60835d9..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000039.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - to_RNA (Seq::NA::DNA) - - - - - 
# File seq.rb, line 99
-                        def to_RNA
-                                Seq::NA::RNA.new( self.tr( 'Tt', 'Uu' ) )
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000040.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000040.html deleted file mode 100644 index 6e79d17..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000040.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - complement (Seq::NA::DNA) - - - - - 
# File seq.rb, line 104
-                        def complement
-                                self.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.html deleted file mode 100644 index 2345f3f..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.html +++ /dev/null @@ -1,217 +0,0 @@ - - - - Class: Seq::NA::RNA [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeq::NA::RNA
In: - - - - - seq.rb - - - - -
- -
Parent: - - - - Seq::NA - - - -
-
- - -
- -
- -
-

-Class containing methods specific for RNA sequences. -

- -
- -
- - -
-

Methods

- -
- - complement   - - residues   - - to_DNA   - -
-
- -
- - - -
- - - - - - -
- -

Public Instance methods

- - -
- - -
- - - - complement() - - - -
- -
- -

-Method that complements RNA sequence including -ambiguity codes. -

- -
-
- - -
- - -
- - - - residues() - - - -
- -
- -

-Method that returns an array of RNA residues. -

- -
-
- - -
- - -
- - - - to_DNA() - - - -
- -
- -

-Method to reverse transcribe RNA to DNA. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000041.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000041.html deleted file mode 100644 index 92655b3..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000041.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - residues (Seq::NA::RNA) - - - - - 
# File seq.rb, line 112
-                        def residues
-                                %w{ A U C G }
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000042.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000042.html deleted file mode 100644 index 7307861..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000042.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - to_DNA (Seq::NA::RNA) - - - - - 
# File seq.rb, line 117
-                        def to_DNA
-                                Seq::NA::DNA.new( self.tr( 'Uu', 'Tt' ) )
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000043.html b/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000043.html deleted file mode 100644 index 7f5d3f2..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000043.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - complement (Seq::NA::RNA) - - - - - 
# File seq.rb, line 122
-                        def complement
-                                self.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
-                        end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/SeqError.html b/code_ruby/Maasha/lib/doc/classes/SeqError.html deleted file mode 100644 index 192b171..0000000 --- a/code_ruby/Maasha/lib/doc/classes/SeqError.html +++ /dev/null @@ -1,117 +0,0 @@ - - - - Class: SeqError [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassSeqError
In: - - - - - seq.rb - - - - -
- -
Parent: - - StandardError - -
-
- - -
- -
- -
-

-Error class for all exceptions to do with Seq. -

- -
- -
- - -
- - - -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.html b/code_ruby/Maasha/lib/doc/classes/Status.html deleted file mode 100644 index d6681d4..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - Class: Status [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassStatus
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - Object - -
-
- - -
- -
- -
-

-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. -

- -
- -
- - -
-

Methods

- -
- - delete   - - get_tmpdir   - - log   - - set   - - set_tmpdir   - -
-
- -
- - - -
- - - - - - -
- -

Public Instance methods

- - -
- - -
- - - - delete() - - - -
- -
- -

-Delete status file. -

- -
-
- - -
- - -
- - - - get_tmpdir() - - - -
- -
- -

-Extract the temporary directory path from the status file, and return this -or nil if not found. -

- -
-
- - -
- - -
- - - - log(exit_status) - - - -
- -
- -

-Write the Biopiece status to the log file. -

- -
-
- - -
- - -
- - - - set() - - - -
- -
- -

-Write the status to a status file. -

- -
-
- - -
- - -
- - - - set_tmpdir(tmpdir_path) - - - -
- -
- -

-Append the a temporary directory path to the status file. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.src/M000025.html b/code_ruby/Maasha/lib/doc/classes/Status.src/M000025.html deleted file mode 100644 index 84e53d7..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.src/M000025.html +++ /dev/null @@ -1,19 +0,0 @@ - - - - set (Status) - - - - - 
# File biopieces.rb, line 474
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.src/M000026.html b/code_ruby/Maasha/lib/doc/classes/Status.src/M000026.html deleted file mode 100644 index 3a81609..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.src/M000026.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - set_tmpdir (Status) - - - - - 
# File biopieces.rb, line 483
-  def set_tmpdir(tmpdir_path)
-    File.open(path, mode="r") do |fh|
-      fh.read.chomp
-    end
-
-    File.open(path, mode="w") do |fh|
-      fh << [status, tmpdir_path].join(";") + "\n"
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.src/M000027.html b/code_ruby/Maasha/lib/doc/classes/Status.src/M000027.html deleted file mode 100644 index a78ea57..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.src/M000027.html +++ /dev/null @@ -1,20 +0,0 @@ - - - - get_tmpdir (Status) - - - - - 
# File biopieces.rb, line 495
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.src/M000028.html b/code_ruby/Maasha/lib/doc/classes/Status.src/M000028.html deleted file mode 100644 index 4f73b4e..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.src/M000028.html +++ /dev/null @@ -1,27 +0,0 @@ - - - - log (Status) - - - - - 
# File biopieces.rb, line 505
-  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
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Status.src/M000029.html b/code_ruby/Maasha/lib/doc/classes/Status.src/M000029.html deleted file mode 100644 index 2e74133..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Status.src/M000029.html +++ /dev/null @@ -1,15 +0,0 @@ - - - - delete (Status) - - - - - 
# File biopieces.rb, line 522
-  def delete
-    File.delete(path)
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/classes/Stream.html b/code_ruby/Maasha/lib/doc/classes/Stream.html deleted file mode 100644 index a1db5ee..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Stream.html +++ /dev/null @@ -1,154 +0,0 @@ - - - - Class: Stream [RDoc Documentation] - - - - - - - - - -
- - - - - - - - - - - - - - - - -
ClassStream
In: - - - - - biopieces.rb - - - - -
- -
Parent: - - IO - -
-
- - -
- -
- -
- - -
-

Methods

- -
- - open   - -
-
- -
- - - -
- - - - - - -
- -

Public Class methods

- - -
- - -
- - - - open(options, mode, stdio) - - - -
- -
- -

-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“]. -

- -
-
- - - -
- - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/classes/Stream.src/M000030.html b/code_ruby/Maasha/lib/doc/classes/Stream.src/M000030.html deleted file mode 100644 index 9a8cbd8..0000000 --- a/code_ruby/Maasha/lib/doc/classes/Stream.src/M000030.html +++ /dev/null @@ -1,21 +0,0 @@ - - - - open (Stream) - - - - - 
# File biopieces.rb, line 547
-  def self.open(options, mode, stdio)
-    if mode == "r"
-      $stdin.tty? ? read(options["stream_in"]) : stdio
-    elsif mode == "w"
-      options["stream_out"] ? self.write(options["stream_out"], options["compress"]) : stdio
-    else
-      raise "Bad mode #{mode}"
-    end
-  end
- - diff --git a/code_ruby/Maasha/lib/doc/created.rid b/code_ruby/Maasha/lib/doc/created.rid deleted file mode 100644 index 36dfd11..0000000 --- a/code_ruby/Maasha/lib/doc/created.rid +++ /dev/null @@ -1,13 +0,0 @@ -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 diff --git a/code_ruby/Maasha/lib/doc/digest_rb.html b/code_ruby/Maasha/lib/doc/digest_rb.html deleted file mode 100644 index 22b22e5..0000000 --- a/code_ruby/Maasha/lib/doc/digest_rb.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - File: digest.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-19 15:41:06 +0100
- - -
Requires
-
-
    - -
  • seq
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/fasta_rb.html b/code_ruby/Maasha/lib/doc/fasta_rb.html deleted file mode 100644 index 1782158..0000000 --- a/code_ruby/Maasha/lib/doc/fasta_rb.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - File: fasta.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-19 09:11:06 +0100
- - -
Requires
-
-
    - -
  • seq
    • - -
  • filesys
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/fastq_rb.html b/code_ruby/Maasha/lib/doc/fastq_rb.html deleted file mode 100644 index 0d97142..0000000 --- a/code_ruby/Maasha/lib/doc/fastq_rb.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - File: fastq.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-19 09:09:52 +0100
- - -
Requires
-
-
    - -
  • seq
    • - -
  • filesys
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/files/biopieces_rb.html b/code_ruby/Maasha/lib/doc/files/biopieces_rb.html deleted file mode 100644 index 0efeadc..0000000 --- a/code_ruby/Maasha/lib/doc/files/biopieces_rb.html +++ /dev/null @@ -1,115 +0,0 @@ - - - - File: biopieces.rb [RDoc Documentation] - - - - - - - - - -
-

biopieces.rb

- - - - - - - - - -
Path:biopieces.rb - -
Last Update:2010-08-17 14:23:28 +0200
-
- - -
- -
- -
-

-Copyright (C) 2007-2010 Martin A. Hansen. -

- -
- -
-

Required files

- -
- - fileutils   - - date   - - optparse   - - open3   - - pp   - -
-
- -
- - -
- - - -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/files/fasta_rb.html b/code_ruby/Maasha/lib/doc/files/fasta_rb.html deleted file mode 100644 index 21a9b00..0000000 --- a/code_ruby/Maasha/lib/doc/files/fasta_rb.html +++ /dev/null @@ -1,112 +0,0 @@ - - - - File: fasta.rb [RDoc Documentation] - - - - - - - - - -
-

fasta.rb

- - - - - - - - - -
Path:fasta.rb - -
Last Update:2010-08-18 21:33:24 +0200
-
- - -
- -
- -
-

-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. -

- -
- -
-

Required files

- -
- - seq   - - zlib   - -
-
- -
- - -
- - - -
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/files/seq_rb.html b/code_ruby/Maasha/lib/doc/files/seq_rb.html deleted file mode 100644 index e080b99..0000000 --- a/code_ruby/Maasha/lib/doc/files/seq_rb.html +++ /dev/null @@ -1,121 +0,0 @@ - - - - File: seq.rb [RDoc Documentation] - - - - - - - - - -
-

seq.rb

- - - - - - - - - -
Path:seq.rb - -
Last Update:2010-08-17 08:33:38 +0200
-
- - -
- -
- -
- - -
- - - -
- -
-

Constants

- -
- - - - - - - - - - - - - - - - - - - - - - - -
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]
-
-
- - - - - - - - - -
- -
-

[Validate]

-
- - - diff --git a/code_ruby/Maasha/lib/doc/filesys_rb.html b/code_ruby/Maasha/lib/doc/filesys_rb.html deleted file mode 100644 index 7d9ac37..0000000 --- a/code_ruby/Maasha/lib/doc/filesys_rb.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - File: filesys.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-18 22:13:22 +0100
- - -
Requires
-
-
    - -
  • zlib
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/fr_class_index.html b/code_ruby/Maasha/lib/doc/fr_class_index.html deleted file mode 100644 index 2557682..0000000 --- a/code_ruby/Maasha/lib/doc/fr_class_index.html +++ /dev/null @@ -1,27 +0,0 @@ - - - - - Classes [RDoc Documentation] - - - - - -
-

Classes

-
- - Fasta
- - FastaError
- -
-
- - diff --git a/code_ruby/Maasha/lib/doc/fr_file_index.html b/code_ruby/Maasha/lib/doc/fr_file_index.html deleted file mode 100644 index 83e8a04..0000000 --- a/code_ruby/Maasha/lib/doc/fr_file_index.html +++ /dev/null @@ -1,25 +0,0 @@ - - - - - Files [RDoc Documentation] - - - - - -
-

Files

-
- - fasta.rb
- -
-
- - diff --git a/code_ruby/Maasha/lib/doc/fr_method_index.html b/code_ruby/Maasha/lib/doc/fr_method_index.html deleted file mode 100644 index 007edaa..0000000 --- a/code_ruby/Maasha/lib/doc/fr_method_index.html +++ /dev/null @@ -1,33 +0,0 @@ - - - - - Methods [RDoc Documentation] - - - - - -
-

Methods

- -
- - diff --git a/code_ruby/Maasha/lib/doc/genbank_rb.html b/code_ruby/Maasha/lib/doc/genbank_rb.html deleted file mode 100644 index 7434343..0000000 --- a/code_ruby/Maasha/lib/doc/genbank_rb.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - File: genbank.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-19 09:19:25 +0100
- - -
Requires
-
-
    - -
  • seq
    • - -
  • filesys
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2010 Martin A. Hansen. -

- -
- -
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a/code_ruby/Maasha/lib/doc/js/quicksearch.js +++ /dev/null @@ -1,114 +0,0 @@ -/** - * - * 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 - * - */ -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 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-} - -/* --- Method classes -------------------------- */ - -.method-detail { - background: #efefef; - padding: 0; - margin-top: 0.5em; - margin-bottom: 1em; - border: 1px dotted #ccc; -} - -.method-heading { - color: black; - background: #ccc; - border-bottom: 1px solid #666; - padding: 0.2em 0.5em 0 0.5em; -} - -.method-signature { - color: black; - background: inherit; -} - -.method-name { - font-weight: bold; -} - -.method-args { - font-style: italic; -} - -.method-description { - padding: 0 0.5em 0 0.5em; -} - -/* --- Source code sections -------------------- */ - -:link.source-toggle, :visited.source-toggle { - font-size: 90%; -} - -div.method-source-code { - background: #262626; - color: #ffdead; - margin: 1em; - padding: 0.5em; - border: 1px dashed #999; - overflow: auto; -} - -div.method-source-code pre { - color: #ffdead; -} - -/* --- Ruby keyword styles --------------------- */ - -.standalone-code { - background: #221111; - color: #ffdead; - overflow: auto; -} - -.ruby-constant { - color: #7fffd4; - background: transparent; -} - -.ruby-keyword { - color: #00ffff; - background: transparent; -} - -.ruby-ivar { - color: #eedd82; - background: transparent; -} - -.ruby-operator { - color: #00ffee; - background: transparent; -} - -.ruby-identifier { - color: #ffdead; - background: transparent; -} - -.ruby-node { - color: #ffa07a; - background: transparent; -} - -.ruby-comment { - color: #b22222; - font-weight: bold; - background: transparent; -} - -.ruby-regexp { - color: #ffa07a; - background: transparent; -} - -.ruby-value { - color: #7fffd4; - background: transparent; -} diff --git a/code_ruby/Maasha/lib/doc/rdoc.css b/code_ruby/Maasha/lib/doc/rdoc.css deleted file mode 100644 index ffe9960..0000000 --- a/code_ruby/Maasha/lib/doc/rdoc.css +++ /dev/null @@ -1,706 +0,0 @@ -/* - * "Darkfish" Rdoc CSS - * $Id: rdoc.css 54 2009-01-27 01:09:48Z deveiant $ - * - * Author: Michael Granger - * - */ - -/* Base Green is: #6C8C22 */ - -*{ padding: 0; margin: 0; } - -body { - background: #efefef; - font: 14px "Helvetica Neue", Helvetica, Tahoma, sans-serif; -} -body.class, body.module, body.file { - margin-left: 40px; -} -body.file-popup { - font-size: 90%; - margin-left: 0; -} - -h1 { - font-size: 300%; - text-shadow: rgba(135,145,135,0.65) 2px 2px 3px; - color: #6C8C22; -} -h2,h3,h4 { margin-top: 1.5em; } - -:link, -:visited { - color: #6C8C22; - text-decoration: none; -} -:link:hover, -:visited:hover { - border-bottom: 1px dotted #6C8C22; -} - -pre { - background: #ddd; - padding: 0.5em 0; -} - - -/* @group Generic Classes */ - -.initially-hidden { - display: none; -} - -.quicksearch-field { - width: 98%; - background: #ddd; - border: 1px solid #aaa; - height: 1.5em; - -webkit-border-radius: 4px; -} -.quicksearch-field:focus { - background: #f1edba; -} - -.missing-docs { - font-size: 120%; - background: white url(images/wrench_orange.png) no-repeat 4px center; - color: #ccc; - line-height: 2em; - border: 1px solid #d00; - opacity: 1; - padding-left: 20px; - text-indent: 24px; - letter-spacing: 3px; - font-weight: bold; - -webkit-border-radius: 5px; - -moz-border-radius: 5px; -} - -.target-section { - border: 2px solid #dcce90; - border-left-width: 8px; - padding: 0 1em; - background: #fff3c2; -} - -/* @end */ - - -/* @group Index Page, Standalone file pages */ -body.indexpage { - margin: 1em 3em; -} -body.indexpage p, -body.indexpage div, -body.file p { - margin: 1em 0; -} - -.indexpage ul, -.file #documentation ul { - line-height: 160%; - list-style: none; -} -.indexpage ul :link, -.indexpage ul :visited { - font-size: 16px; -} - -.indexpage li, -.file #documentation li { - padding-left: 20px; - background: url(images/bullet_black.png) no-repeat left 4px; -} -.indexpage li.module { - background: url(images/package.png) no-repeat left 4px; -} -.indexpage li.class { - background: url(images/ruby.png) no-repeat left 4px; -} -.indexpage li.file { - background: url(images/page_white_text.png) no-repeat left 4px; -} -.file li p, -.indexpage li p { - margin: 0 0; -} - -/* @end */ - -/* @group Top-Level Structure */ - -.class #metadata, -.file #metadata, -.module #metadata { - float: left; - width: 260px; -} - -.class #documentation, -.file #documentation, -.module #documentation { - margin: 2em 1em 5em 300px; - min-width: 340px; -} - -.file #metadata { - margin: 0.8em; -} - -#validator-badges { - clear: both; - margin: 1em 1em 2em; -} - -/* @end */ - -/* @group Metadata Section */ -#metadata .section { - background-color: #dedede; - -moz-border-radius: 5px; - -webkit-border-radius: 5px; - border: 1px solid #aaa; - margin: 0 8px 16px; - font-size: 90%; - overflow: hidden; -} -#metadata h3.section-header { - margin: 0; - padding: 2px 8px; - background: #ccc; - color: #666; - -moz-border-radius-topleft: 4px; - -moz-border-radius-topright: 4px; - -webkit-border-top-left-radius: 4px; - -webkit-border-top-right-radius: 4px; - border-bottom: 1px solid #aaa; -} -#metadata #home-section h3.section-header { 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background-color: #dedede; - color: #333; - font-size: 150%; - border: 1px solid #bbb; - -moz-border-radius: 3px; - -webkit-border-radius: 3px; -} - -#constants-list > dl, -#attributes-list > dl { - margin: 1em 0 2em; - border: 0; -} -#constants-list > dl dt, -#attributes-list > dl dt { - padding-left: 0; - font-weight: bold; - font-family: Monaco, "Andale Mono"; - background: inherit; -} -#constants-list > dl dt a, -#attributes-list > dl dt a { - color: inherit; -} -#constants-list > dl dd, -#attributes-list > dl dd { - margin: 0 0 1em 0; - padding: 0; - color: #666; -} - -/* @group Method Details */ - -#documentation .method-source-code { - display: none; -} - -#documentation .method-detail { - margin: 0.5em 0; - padding: 0.5em 0; - cursor: pointer; -} -#documentation .method-detail:hover { - background-color: #f1edba; -} -#documentation .method-heading { - position: relative; - padding: 2px 4px 0 20px; - font-size: 125%; - font-weight: bold; - color: #333; - background: url(images/brick.png) no-repeat left bottom; -} -#documentation .method-heading :link, -#documentation .method-heading :visited { - color: inherit; -} -#documentation .method-click-advice { - position: absolute; - top: 2px; - right: 5px; - font-size: 10px; - color: #9b9877; - visibility: hidden; - padding-right: 20px; - line-height: 20px; - background: url(images/zoom.png) no-repeat right top; -} -#documentation .method-detail:hover .method-click-advice { - visibility: visible; -} - -#documentation .method-alias .method-heading { - color: #666; - background: url(images/brick_link.png) no-repeat left bottom; -} - -#documentation .method-description, -#documentation .aliases { - margin: 0 20px; - line-height: 1.2em; - color: #666; -} -#documentation .aliases { - padding-top: 4px; - font-style: italic; - cursor: default; -} -#documentation .method-description p { - padding: 0; -} -#documentation .method-description p + p { - margin-bottom: 0.5em; -} -#documentation .method-description ul { - margin-left: 1.5em; -} - -#documentation .attribute-method-heading { - background: url(images/tag_green.png) no-repeat left bottom; -} -#documentation #attribute-method-details .method-detail:hover { - background-color: transparent; - cursor: default; -} -#documentation .attribute-access-type { - font-size: 60%; - text-transform: uppercase; - vertical-align: super; - padding: 0 2px; -} -/* @end */ - -/* @end */ - - - -/* @group Source Code */ - -div.method-source-code { - background: #262626; - color: #efefef; - margin: 1em; - padding: 0.5em; - border: 1px dashed #999; - overflow: hidden; -} - -div.method-source-code pre { - background: inherit; - padding: 0; - color: white; - overflow: auto; -} - -/* @group Ruby keyword styles */ - -.ruby-constant { color: #7fffd4; background: transparent; } -.ruby-keyword { color: #00ffff; background: transparent; } -.ruby-ivar { color: #eedd82; background: transparent; } -.ruby-operator { color: #00ffee; background: transparent; } -.ruby-identifier { color: #ffdead; background: transparent; } -.ruby-node { color: #ffa07a; background: transparent; } -.ruby-comment { color: #b22222; font-weight: bold; background: transparent; } -.ruby-regexp { color: #ffa07a; background: transparent; } -.ruby-value { color: #7fffd4; background: transparent; } - -/* @end */ -/* @end */ - - -/* @group File Popup Contents */ - -.file #metadata, -.file-popup #metadata { -} - -.file-popup dl { - font-size: 80%; - padding: 0.75em; - background-color: #dedede; - color: #333; - border: 1px solid #bbb; - -moz-border-radius: 3px; - -webkit-border-radius: 3px; -} -.file dt { - font-weight: bold; - padding-left: 22px; - line-height: 20px; - background: url(images/page_white_width.png) no-repeat left top; -} -.file dt.modified-date { - background: url(images/date.png) no-repeat left top; -} -.file dt.requires { - background: url(images/plugin.png) no-repeat left top; -} -.file dt.scs-url { - background: url(images/wrench.png) no-repeat left top; -} - -.file dl dd { - margin: 0 0 1em 0; -} -.file #metadata dl dd ul { - list-style: circle; - margin-left: 20px; - padding-top: 0; -} -.file #metadata dl dd ul li { -} - - -.file h2 { - margin-top: 2em; - padding: 0.75em 0.5em; - background-color: #dedede; - color: #333; - font-size: 120%; - border: 1px solid #bbb; - -moz-border-radius: 3px; - -webkit-border-radius: 3px; -} - -/* @end */ - - - - -/* @group ThickBox Styles */ -#TB_window { - font: 12px Arial, Helvetica, sans-serif; - color: #333333; -} - -#TB_secondLine { - font: 10px Arial, Helvetica, sans-serif; - color:#666666; -} - -#TB_window :link, -#TB_window :visited { color: #666666; } -#TB_window :link:hover, -#TB_window :visited:hover { color: #000; } -#TB_window :link:active, -#TB_window :visited:active { color: #666666; } -#TB_window :link:focus, -#TB_window :visited:focus { color: #666666; } - -#TB_overlay { - position: fixed; - z-index:100; - 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; -} - -#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; -} - -#TB_ajaxWindowTitle{ - float:left; - padding:7px 0 5px 10px; - margin-bottom:1px; - font-size: 22px; -} - -#TB_title{ - background-color: #6C8C22; - color: #dedede; - height:40px; -} -#TB_title :link, -#TB_title :visited { - color: white !important; - border-bottom: 1px dotted #dedede; -} - -#TB_ajaxContent{ - clear:both; - padding:2px 15px 15px 15px; - overflow:auto; - text-align:left; - line-height:1.4em; -} - -#TB_ajaxContent.TB_modal{ - padding:15px; -} - -#TB_ajaxContent p{ - padding:5px 0px 5px 0px; -} - -#TB_load{ - position: fixed; - display:none; - height:13px; - width:208px; - z-index:103; - top: 50%; - left: 50%; - margin: -6px 0 0 -104px; /* -height/2 0 0 -width/2 */ -} - -* 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'); -} - -#TB_HideSelect{ - z-index:99; - position:fixed; - top: 0; - left: 0; - background-color:#fff; - border:none; - filter:alpha(opacity=0); - -moz-opacity: 0; - opacity: 0; - height:100%; - width:100%; -} - -* html #TB_HideSelect { /* ie6 hack */ - position: absolute; - height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px'); -} - -#TB_iframeContent{ - clear:both; - border:none; - margin-bottom:-1px; - margin-top:1px; - _margin-bottom:1px; -} - -/* @end */ - -/* @group Debugging Section */ - -#debugging-toggle { - text-align: center; -} -#debugging-toggle img { - cursor: pointer; -} - -#rdoc-debugging-section-dump { - display: none; - margin: 0 2em 2em; - background: #ccc; - border: 1px solid #999; -} - - - -/* @end */ diff --git a/code_ruby/Maasha/lib/doc/seq_rb.html b/code_ruby/Maasha/lib/doc/seq_rb.html deleted file mode 100644 index 3c50f10..0000000 --- a/code_ruby/Maasha/lib/doc/seq_rb.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - File: seq.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-03-19 16:29:08 +0100
- - -
Requires
-
-
    - -
  • amatch
    • - -
  • digest
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2007-2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Maasha/lib/doc/sff_rb.html b/code_ruby/Maasha/lib/doc/sff_rb.html deleted file mode 100644 index 294f9a0..0000000 --- a/code_ruby/Maasha/lib/doc/sff_rb.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - File: sff.rb [RDoc Documentation] - - - - - - - - - - -
-
-
Last Modified
-
2011-02-11 19:55:38 +0100
- - -
Requires
-
-
    - -
  • base36
    • - -
-
- - - -
-
- -
- -
-

Description

-

-Copyright (C) 2011 Martin A. Hansen. -

- -
- -
- - - diff --git a/code_ruby/Sfern/test_module.rb b/code_ruby/Sfern/test_module.rb deleted file mode 100755 index 681661c..0000000 --- a/code_ruby/Sfern/test_module.rb +++ /dev/null @@ -1,7 +0,0 @@ -class Test - puts "Modules Test2 loaded" - - def greet_world - puts "World" - end -end diff --git a/code_ruby/Maasha/lib/base36.rb b/code_ruby/lib/maasha/base36.rb similarity index 100% rename from code_ruby/Maasha/lib/base36.rb rename to code_ruby/lib/maasha/base36.rb diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/lib/maasha/biopieces.rb similarity index 100% rename from code_ruby/Maasha/lib/biopieces.rb rename to code_ruby/lib/maasha/biopieces.rb diff --git a/code_ruby/Maasha/lib/bitarray.rb b/code_ruby/lib/maasha/bitarray.rb similarity index 100% rename from code_ruby/Maasha/lib/bitarray.rb rename to code_ruby/lib/maasha/bitarray.rb diff --git a/code_ruby/Maasha/lib/bits.rb b/code_ruby/lib/maasha/bits.rb similarity index 100% rename from code_ruby/Maasha/lib/bits.rb rename to code_ruby/lib/maasha/bits.rb diff --git a/code_ruby/lib/maasha/boulder.rb b/code_ruby/lib/maasha/boulder.rb new file mode 100644 index 0000000..2a484a4 --- /dev/null +++ b/code_ruby/lib/maasha/boulder.rb @@ -0,0 +1,78 @@ +# 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 diff --git a/code_ruby/Maasha/lib/digest.rb b/code_ruby/lib/maasha/digest.rb similarity index 100% rename from code_ruby/Maasha/lib/digest.rb rename to code_ruby/lib/maasha/digest.rb diff --git a/code_ruby/Maasha/lib/fasta.rb b/code_ruby/lib/maasha/fasta.rb similarity index 97% rename from code_ruby/Maasha/lib/fasta.rb rename to code_ruby/lib/maasha/fasta.rb index e972751..f57a622 100644 --- a/code_ruby/Maasha/lib/fasta.rb +++ b/code_ruby/lib/maasha/fasta.rb @@ -22,8 +22,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'seq' -require 'filesys' +require 'maasha/seq' +require 'maasha/filesys' # Error class for all exceptions to do with FASTA. class FastaError < StandardError; end diff --git a/code_ruby/Maasha/lib/fastq.rb b/code_ruby/lib/maasha/fastq.rb similarity index 97% rename from code_ruby/Maasha/lib/fastq.rb rename to code_ruby/lib/maasha/fastq.rb index a1eb86c..b3ba85f 100644 --- a/code_ruby/Maasha/lib/fastq.rb +++ b/code_ruby/lib/maasha/fastq.rb @@ -22,8 +22,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'seq' -require 'filesys' +require 'maasha/seq' +require 'maasha/filesys' # Error class for all exceptions to do with FASTQ. class FastqError < StandardError; end diff --git a/code_ruby/Maasha/lib/filesys.rb b/code_ruby/lib/maasha/filesys.rb similarity index 100% rename from code_ruby/Maasha/lib/filesys.rb rename to code_ruby/lib/maasha/filesys.rb diff --git a/code_ruby/Maasha/lib/genbank.rb b/code_ruby/lib/maasha/genbank.rb similarity index 99% rename from code_ruby/Maasha/lib/genbank.rb rename to code_ruby/lib/maasha/genbank.rb index bb40d3d..a6ec292 100644 --- a/code_ruby/Maasha/lib/genbank.rb +++ b/code_ruby/lib/maasha/genbank.rb @@ -22,8 +22,8 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'seq' -require 'filesys' +require 'maasha/seq' +require 'maasha/filesys' # Error class for all exceptions to do with Genbank. class GenbankError < StandardError; end diff --git a/code_ruby/Maasha/lib/patscan.rb b/code_ruby/lib/maasha/patscan.rb similarity index 99% rename from code_ruby/Maasha/lib/patscan.rb rename to code_ruby/lib/maasha/patscan.rb index e0ae706..4e31398 100644 --- a/code_ruby/Maasha/lib/patscan.rb +++ b/code_ruby/lib/maasha/patscan.rb @@ -22,7 +22,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'filesys' +require 'maasha/filesys' require 'open3' # Module containing code to locate nucleotide patterns in sequences allowing for diff --git a/code_ruby/Maasha/lib/patternmatcher.rb b/code_ruby/lib/maasha/patternmatcher.rb similarity index 100% rename from code_ruby/Maasha/lib/patternmatcher.rb rename to code_ruby/lib/maasha/patternmatcher.rb diff --git a/code_ruby/Maasha/lib/prodigal.rb b/code_ruby/lib/maasha/prodigal.rb similarity index 99% rename from code_ruby/Maasha/lib/prodigal.rb rename to code_ruby/lib/maasha/prodigal.rb index 9ddbf79..35b4992 100644 --- a/code_ruby/Maasha/lib/prodigal.rb +++ b/code_ruby/lib/maasha/prodigal.rb @@ -22,7 +22,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'genbank' +require 'maasha/genbank' # Class for running the Prodigal gene finder. # http://prodigal.ornl.gov/ diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/lib/maasha/seq.rb similarity index 99% rename from code_ruby/Maasha/lib/seq.rb rename to code_ruby/lib/maasha/seq.rb index 1227ac4..21e6e07 100644 --- a/code_ruby/Maasha/lib/seq.rb +++ b/code_ruby/lib/maasha/seq.rb @@ -22,9 +22,9 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'digest' -#require 'patscan' -require 'patternmatcher' +require 'maasha/digest' +require 'maasha/patternmatcher' +#require 'maasha/patscan' # Residue alphabets DNA = %w[a t c g] diff --git a/code_ruby/Maasha/lib/sff.rb b/code_ruby/lib/maasha/sff.rb similarity index 99% rename from code_ruby/Maasha/lib/sff.rb rename to code_ruby/lib/maasha/sff.rb index a3497f0..0a9d2a1 100644 --- a/code_ruby/Maasha/lib/sff.rb +++ b/code_ruby/lib/maasha/sff.rb @@ -22,7 +22,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'base36' +require 'maasha/base36' # Error class for all exceptions to do with SFF. class SFFError < StandardError; end diff --git a/code_ruby/Maasha/test/test_base36.rb b/code_ruby/test/maasha/test_base36.rb similarity index 98% rename from code_ruby/Maasha/test/test_base36.rb rename to code_ruby/test/maasha/test_base36.rb index c966900..683d267 100755 --- a/code_ruby/Maasha/test/test_base36.rb +++ b/code_ruby/test/maasha/test_base36.rb @@ -26,7 +26,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'test/unit' -require 'base36' +require 'maasha/base36' require 'pp' class Base36Test < Test::Unit::TestCase diff --git a/code_ruby/Maasha/test/test_biopieces.rb b/code_ruby/test/maasha/test_biopieces.rb similarity index 99% rename from code_ruby/Maasha/test/test_biopieces.rb rename to code_ruby/test/maasha/test_biopieces.rb index be702b5..49d10a5 100755 --- a/code_ruby/Maasha/test/test_biopieces.rb +++ b/code_ruby/test/maasha/test_biopieces.rb @@ -26,7 +26,8 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'test/unit' -require 'biopieces' +require 'maasha/biopieces' +require 'stringio' require 'pp' TYPES = %w[flag string list int uint float file file! files files! dir dir! genome] diff --git a/code_ruby/Maasha/test/test_bitarray.rb b/code_ruby/test/maasha/test_bitarray.rb similarity index 99% rename from code_ruby/Maasha/test/test_bitarray.rb rename to code_ruby/test/maasha/test_bitarray.rb index 5a3a88a..4745401 100755 --- a/code_ruby/Maasha/test/test_bitarray.rb +++ b/code_ruby/test/maasha/test_bitarray.rb @@ -26,7 +26,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'bitarray' +require 'maasha/bitarray' require 'test/unit' require 'pp' diff --git a/code_ruby/Maasha/test/test_bits.rb b/code_ruby/test/maasha/test_bits.rb similarity index 99% rename from code_ruby/Maasha/test/test_bits.rb rename to code_ruby/test/maasha/test_bits.rb index f817dc2..5a589f5 100755 --- a/code_ruby/Maasha/test/test_bits.rb +++ b/code_ruby/test/maasha/test_bits.rb @@ -26,7 +26,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'bits' +require 'maasha/bits' require 'test/unit' require 'pp' diff --git a/code_ruby/test/maasha/test_boulder.rb b/code_ruby/test/maasha/test_boulder.rb new file mode 100755 index 0000000..a0afe99 --- /dev/null +++ b/code_ruby/test/maasha/test_boulder.rb @@ -0,0 +1,75 @@ +#!/usr/bin/env ruby +$:.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 diff --git a/code_ruby/Maasha/test/test_digest.rb b/code_ruby/test/maasha/test_digest.rb similarity index 96% rename from code_ruby/Maasha/test/test_digest.rb rename to code_ruby/test/maasha/test_digest.rb index 9db221a..1e09f96 100755 --- a/code_ruby/Maasha/test/test_digest.rb +++ b/code_ruby/test/maasha/test_digest.rb @@ -1,6 +1,6 @@ #!/usr/bin/env ruby -require 'seq' +require 'maasha/seq' require 'test/unit' require 'pp' diff --git a/code_ruby/Maasha/test/test_fasta.rb b/code_ruby/test/maasha/test_fasta.rb similarity index 99% rename from code_ruby/Maasha/test/test_fasta.rb rename to code_ruby/test/maasha/test_fasta.rb index 23672af..d5ba7bd 100755 --- a/code_ruby/Maasha/test/test_fasta.rb +++ b/code_ruby/test/maasha/test_fasta.rb @@ -26,7 +26,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'test/unit' -require 'fasta' +require 'maasha/fasta' require 'stringio' require 'pp' diff --git a/code_ruby/Maasha/test/test_fastq.rb b/code_ruby/test/maasha/test_fastq.rb similarity index 98% rename from code_ruby/Maasha/test/test_fastq.rb rename to code_ruby/test/maasha/test_fastq.rb index c06a07e..2316fc7 100755 --- a/code_ruby/Maasha/test/test_fastq.rb +++ b/code_ruby/test/maasha/test_fastq.rb @@ -26,7 +26,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'test/unit' -require 'fastq' +require 'maasha/fastq' require 'stringio' require 'pp' diff --git a/code_ruby/Maasha/test/test_genbank.rb b/code_ruby/test/maasha/test_genbank.rb similarity index 97% rename from code_ruby/Maasha/test/test_genbank.rb rename to code_ruby/test/maasha/test_genbank.rb index 3c46386..8f36440 100755 --- a/code_ruby/Maasha/test/test_genbank.rb +++ b/code_ruby/test/maasha/test_genbank.rb @@ -26,8 +26,8 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'genbank' -require 'seq' +require 'maasha/genbank' +require 'maasha/seq' require 'test/unit' require 'pp' diff --git a/code_ruby/Maasha/test/test_patternmatcher.rb b/code_ruby/test/maasha/test_patternmatcher.rb similarity index 99% rename from code_ruby/Maasha/test/test_patternmatcher.rb rename to code_ruby/test/maasha/test_patternmatcher.rb index 7993862..9a7a50e 100755 --- a/code_ruby/Maasha/test/test_patternmatcher.rb +++ b/code_ruby/test/maasha/test_patternmatcher.rb @@ -25,7 +25,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -require 'seq' +require 'maasha/seq' require 'test/unit' require 'pp' diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/test/maasha/test_seq.rb similarity index 99% rename from code_ruby/Maasha/test/test_seq.rb rename to code_ruby/test/maasha/test_seq.rb index e463e6f..5e79a0f 100755 --- a/code_ruby/Maasha/test/test_seq.rb +++ b/code_ruby/test/maasha/test_seq.rb @@ -1,6 +1,6 @@ #!/usr/bin/env ruby -require 'seq' +require 'maasha/seq' require 'test/unit' require 'pp' -- 2.39.5