#!/usr/bin/env ruby
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# 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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+require 'maasha/biopieces'
+require 'maasha/fasta'
+require 'maasha/usearch'
-require 'biopieces'
-require 'fasta'
-
-class Uclust
- include Enumerable
-
- def initialize(infile, outfile, options)
- @infile = infile
- @outfile = outfile
- @options = options
- @command = []
-
- @command << "--rev" if @options[:comp]
- end
-
- # Method that calls Uclusts sorting for sorting a FASTA file
- # according to decending sequence length.
- def sort
- @command << "uclust --sort #{@infile} --output #{@infile}.sort"
-
- execute
-
- File.rename "#{@infile}.sort", @infile
- end
-
- def ublast
- # uclust --ublast query_seqs.fasta --db database.fasta --blast6out filename --evalue E
- @options[:e_val] = 10 unless @options[:e_val]
- @command << "uclust --ublast #{@infile} --db #{@options[:database]} --blast6out #{@outfile} --evalue #{@options[:e_val]}"
-
- execute
- end
-
- # Method to execute database search.
- def usearch
- # uclust --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
- @command << "uclust --query #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
- @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
-
- execute
- end
+casts = []
+casts << {long: 'no_sort', short: 'n', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'comp', short: 'c', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'identity', short: 'i', type: 'float', mandatory: true, default: 0.9, allowed: nil, disallowed: nil}
- # Method to execute clustering de novo.
- def uclust
- # uclust --input seqs_sorted.fasta --uc results.uc --id 0.90
- @command << "uclust --input #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
+options = Biopieces.options_parse(ARGV, casts)
- execute
- end
+tmpdir = Biopieces.mktmpdir
+file_records = File.join(tmpdir, "data.stream")
+file_fasta = File.join(tmpdir, "in.fna")
+file_uclust = File.join(tmpdir, "out.uc")
- # Method to execute clustering to database plus de novo if not matched.
- def usearch_uclust
- # uclust --input seqs_sorted.fasta --lib db.fasta --uc results.uc --id 0.90
- @command << "uclust --input #{@infile} --lib #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
- @command << "--lib #{@options[:database]}" if @options.has_key? :database
+Biopieces.open(options[:stream_in], file_records) do |input, output|
+ Fasta.open(file_fasta, 'w') do |fasta_io|
+ input.each_record do |record|
+ output.puts record
- 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")
-
- record[:REC_TYPE] = "UCLUST"
- record[:TYPE] = fields[0]
- record[:CLUSTER] = fields[1]
- record[:SEQ_LEN] = fields[2]
- record[:IDENT] = fields[3]
- record[:STRAND] = fields[4]
- record[:Q_BEG] = fields[5]
- record[:S_BEG] = fields[6]
- record[:CIGAR] = fields[7]
- record[:Q_ID] = fields[8]
- record[:S_ID] = fields[9]
-
- yield record
- end
+ if record[:SEQ_NAME] and record[:SEQ]
+ fasta_io.puts Seq.new_bp(record).to_fasta
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 << "> /dev/null 2>&1" unless @options[:verbose]
- command = @command.join(" ")
- system(command)
- raise "Command failed: #{command}" unless $?.success?
-
- @command = []
- end
end
-ok_methods = "ublast,usearch,uclust,usearch_uclust"
-
-casts = []
-casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'method', :short=>'m', :type=>'string', :mandatory=>true, :default=>"uclust", :allowed=>ok_methods, :disallowed=>nil}
-casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'comp', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.9, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'e_val', :short=>'e', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+us = Usearch.new(file_fasta, file_uclust, options)
-bp = Biopieces.new
+us.sortbylength unless options[:no_sort]
+us.cluster_smallmem
-options = bp.parse(ARGV, casts)
+hash = {}
-tmpdir = bp.mktmpdir
-infile = "#{tmpdir}/in.fna"
-outfile = "#{tmpdir}/out.uc"
-
-Fasta.open(infile, mode="w") do |fasta_io|
- bp.each_record do |record|
- bp.puts record
- fasta_io.puts record
- end
+us.each_cluster do |cluster|
+ hash[cluster[:Q_ID].to_sym] = cluster.dup
end
-uclust = Uclust.new(infile, outfile, options)
-uclust.sort unless options[:no_sort]
-
-case options[:method].to_s
-when "ublast" then uclust.ublast
-when "usearch" then uclust.usearch
-when "uclust" then uclust.uclust
-when "usearch_uclust" then uclust.usearch_uclust
-else raise "Unknown method: #{options[:method]}"
-end
+Biopieces.open(file_records, options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ_NAME] and record[:SEQ]
+ if hash[record[:SEQ_NAME].to_sym]
+ 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
-uclust.each do |record|
- bp.puts record
+ output.puts record
+ end
end
projects / biopieces.git / blobdiff