#!/usr/bin/env ruby
-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2012 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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Assemble sequences in the stream using IDBA.
+# Assemble sequences in the stream using IDBA-UD.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
casts = []
casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'scaffold', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>20, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>100, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cover', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'clean', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean', :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
-file_fasta = File.join(options[:directory], "IDBA") + ".fna"
+file_fasta = File.join(options[:directory], "IDBA-UD") + ".fna"
count = 0
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(file_fasta, mode="w") do |fasta_io|
+ Fasta.open(file_fasta, "w") do |fasta_io|
input.each_record do |record|
- if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
- if record[:SEQ_NAME] =~ /1$/
- record[:SEQ_NAME] = "read#{count}/1"
- else
- record[:SEQ_NAME] = "read#{count}/2"
-
- count += 1
- end
- end
+ if record[:SEQ_NAME] and record[:SEQ]
+ seq = Seq.new_bp(record)
- fasta_io.puts record
+ fasta_io.puts seq.to_fasta
+ end
end
end
unless File.size(file_fasta) == 0
- prefix = File.join(options[:directory], "IDBA")
+ prefix = File.join(options[:directory], "IDBA-UD")
commands = []
commands << "nice -n 19"
- commands << "idba"
+ commands << "idba_ud"
commands << "--read #{file_fasta}"
- commands << "--output #{prefix}"
- commands << "--scaffold" if options[:scaffold]
+ commands << "--out #{prefix}"
commands << "--mink #{options[:kmer_min]}"
commands << "--maxk #{options[:kmer_max]}"
- commands << "--minCount #{options[:count_min]}"
- commands << "--cover #{options[:cover]}"
- commands << "--minPairs #{options[:pairs_min]}"
- commands << "--prefixLength #{options[:prefix_len]}"
+ commands << "--min_count #{options[:count_min]}"
+ commands << "--min_pairs #{options[:pairs_min]}"
+ commands << "--prefix #{options[:prefix_len]}"
+ commands << "--num_threads #{options[:cpus]}"
commands << "> /dev/null 2>&1" unless options[:verbose]
command = commands.join(" ")
- begin
- system(command)
- raise "Command failed: #{command}" unless $?.success?
- rescue
- $stderr.puts "Command failed: #{command}"
- end
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
- if options[:scaffold]
- file_contig = File.join(options[:directory], "IDBA") + "-contig-mate.fa"
- else
- file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
- end
+ file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa")
Fasta.open(file_contig, mode="r") do |fasta_io|
fasta_io.each do |entry|