require 'maasha/biopieces'
require 'maasha/fasta'
-
-SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
-
-class Uclust
- include Enumerable
-
- def initialize(infile, outfile, options)
- @infile = infile
- @outfile = outfile
- @options = options
- @command = []
- end
-
- # Method that calls Usearch sorting for sorting a FASTA file
- # according to decending sequence length.
- def sort
- # usearch -sort seqs.fasta -output seqs.sorted.fasta
- if File.size(@infile) < SORT_LIMIT
- @command << "usearch --sort #{@infile} --output #{@infile}.sort"
- else
- @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
- end
-
- execute
-
- File.rename "#{@infile}.sort", @infile
- end
-
- # Method to execute clustering de novo.
- def cluster
- @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
-
- execute
- end
-
- # Method to parse a Uclust .uc file and for each line of data
- # yield a Biopiece record.
- def each
- record = {}
-
- File.open(@outfile, mode="r") do |ios|
- ios.each_line do |line|
- if line !~ /^#/
- fields = line.chomp.split("\t")
-
- next if fields[0] == 'C'
-
- record[:TYPE] = fields[0]
- record[:CLUSTER] = fields[1].to_i
- record[:IDENT] = fields[3].to_f
- record[:Q_ID] = fields[8]
-
- yield record
- end
- end
- end
-
- self # conventionally
- end
-
- private
-
- # Method to execute a command using a system() call.
- # The command is composed of bits from the @command variable.
- def execute
- @command.unshift "nice -n 19"
- @command << "--rev" if @options[:comp]
- @command << "> /dev/null 2>&1" unless @options[:verbose]
- command = @command.join(" ")
- system(command)
- raise "Command failed: #{command}" unless $?.success?
-
- @command = []
- end
-end
+require 'maasha/usearch'
casts = []
casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
end
end
-uc = Uclust.new(file_fasta, file_uclust, options)
-uc.sort unless options[:no_sort]
-uc.cluster
+us = Usearch.new(file_fasta, file_uclust, options)
+us.sort_length unless options[:no_sort]
+us.cluster
hash = {}
-uc.each do |record|
+us.each_cluster do |record|
hash[record[:Q_ID].to_sym] = record.dup
end
input.each_record do |record|
if record.has_key? :SEQ_NAME and record.has_key? :SEQ
if hash.has_key? record[:SEQ_NAME].to_sym
- uc = hash[record[:SEQ_NAME].to_sym]
- record[:CLUSTER] = uc[:CLUSTER].to_i
- record[:IDENT] = uc[:IDENT].to_i
- record[:IDENT] = '*' if uc[:TYPE] == 'S'
+ us = hash[record[:SEQ_NAME].to_sym]
+ record[:CLUSTER] = us[:CLUSTER].to_i
+ record[:IDENT] = us[:IDENT].to_i
+ record[:IDENT] = '*' if us[:TYPE] == 'S'
end
end
require 'maasha/biopieces'
require 'maasha/fasta'
-
-class Usearch
- include Enumerable
-
- def initialize(infile, outfile, options)
- @infile = infile
- @outfile = outfile
- @options = options
- @command = []
- end
-
- # Method to execute database search.
- def usearch
- @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
- @command << "--userfields target+tloz+thiz+query+bits+strand"
- @command << "--id #{@options[:identity]}" if @options.has_key? :identity
- @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
-
- execute
- end
-
- # Method to parse a Useach .uc file and for each line of data
- # yield a Biopiece record.
- def each
- record = {}
-
- File.open(@outfile, mode="r") do |ios|
- ios.gets # skip comment line
- ios.each_line do |line|
- fields = line.chomp.split("\t")
-
- record[:REC_TYPE] = "USEARCH"
- record[:S_ID] = fields[0]
- record[:S_BEG] = fields[1].to_i
- record[:S_END] = fields[2].to_i
- record[:Q_ID] = fields[3]
- record[:SCORE] = fields[4].to_f
- record[:STRAND] = fields[5]
-
- yield record
- end
- end
-
- self # conventionally
- end
-
- private
-
- # Method to execute a command using a system() call.
- # The command is composed of bits from the @command variable.
- def execute
- @command.unshift "nice -n 19"
- @command << "--rev"
- @command << "> /dev/null 2>&1" unless @options[:verbose]
- command = @command.join(" ")
- system(command)
- raise "Command failed: #{command}" unless $?.success?
-
- @command = []
- end
-end
+require 'maasha/usearch'
casts = []
casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
end
end
- uc = Usearch.new(infile, outfile, options)
+ us = Usearch.new(infile, outfile, options)
- uc.usearch
+ us.usearch
- uc.each do |record|
+ us.each_hit do |record|
output.puts record
end
end
--- /dev/null
+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/fasta'
+
+# Error class for all exceptions to do with Usearch.
+class UsearchError < StandardError; end
+
+SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
+
+class Usearch
+ include Enumerable
+
+ def initialize(infile, outfile, options)
+ @infile = infile
+ @outfile = outfile
+ @options = options
+ @command = []
+ end
+
+ # Method that calls Usearch sorting for sorting a FASTA file
+ # according to decending sequence length.
+ def sort_length
+ # usearch -sort seqs.fasta -output seqs.sorted.fasta
+ if File.size(@infile) < SORT_LIMIT
+ @command << "usearch --sort #{@infile} --output #{@infile}.sort"
+ else
+ @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
+ end
+
+ execute
+
+ File.rename "#{@infile}.sort", @infile
+ end
+
+ # Method that calls Usearch sorting for sorting a FASTA file
+ # according to cluster size.
+ def sort_size
+ # usearch -sortsize seqs.fasta -output seqs.sorted.fasta
+ @command << "usearch --sortsize #{@infile} --output #{@infile}.sort"
+
+ execute
+
+ File.rename "#{@infile}.sort", @infile
+ end
+
+ # Method to execute clustering de novo.
+ def cluster
+ @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
+
+ execute
+ end
+
+ # Method to execute database search.
+ def usearch
+ @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
+ @command << "--userfields target+tloz+thiz+query+bits+strand"
+ @command << "--id #{@options[:identity]}" if @options.has_key? :identity
+ @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
+ @command << "--rev"
+
+ execute
+ end
+
+ # Method to parse a Uclust .uc file and for each line of data
+ # yield a Biopiece record.
+ def each_cluster
+ record = {}
+
+ File.open(@outfile, mode="r") do |ios|
+ ios.each_line do |line|
+ if line !~ /^#/
+ fields = line.chomp.split("\t")
+
+ next if fields[0] == 'C'
+
+ record[:TYPE] = fields[0]
+ record[:CLUSTER] = fields[1].to_i
+ record[:IDENT] = fields[3].to_f
+ record[:Q_ID] = fields[8]
+
+ yield record
+ end
+ end
+ end
+
+ self # conventionally
+ end
+
+ # Method to parse a Useach user defined tabular file and for each line of data
+ # yield a Biopiece record.
+ def each_hit
+ record = {}
+
+ File.open(@outfile, mode="r") do |ios|
+ ios.gets # skip comment line
+ ios.each_line do |line|
+ fields = line.chomp.split("\t")
+
+ record[:REC_TYPE] = "USEARCH"
+ record[:S_ID] = fields[0]
+ record[:S_BEG] = fields[1].to_i
+ record[:S_END] = fields[2].to_i
+ record[:Q_ID] = fields[3]
+ record[:SCORE] = fields[4].to_f
+ record[:STRAND] = fields[5]
+
+ yield record
+ end
+ end
+
+ self # conventionally
+ end
+
+ private
+
+ # Method to execute a command using a system() call.
+ # The command is composed of bits from the @command variable.
+ def execute
+ @command.unshift "nice -n 19"
+ @command << "--rev" if @options[:comp]
+ @command << "> /dev/null 2>&1" unless @options[:verbose]
+ command = @command.join(" ")
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ @command = []
+ end
+end
+
+__END__
+
projects / biopieces.git / commitdiff