#!/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.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'biopieces'
-require 'fasta'
-require 'pp'
-
-ok_methods = "ublast,usearch,uclust,usearch_uclust"
+require 'maasha/biopieces'
+require 'maasha/fasta'
casts = []
-casts << {:long=>'name', :short=>'n', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-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=>'k_value_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'k_value_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :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=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-
-bp = Biopieces.new
+casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :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=>'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=>'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 = bp.parse(ARGV, casts)
+options = Biopieces.options_parse(ARGV, casts)
Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
-file_fasta = [options[:directory], options[:name] ].join(File::SEPARATOR) + ".fna"
-
-Fasta.open(file_fasta, mode="w") do |fasta_io|
- bp.each_record do |record|
- fasta_io.puts record
- end
+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, "w") do |fasta_io|
+ input.each_record do |record|
+ if record[:SEQ_NAME] and record[:SEQ]
+ seq = Seq.new_bp(record)
+
+ fasta_io.puts seq.to_fasta
+ end
+ end
+ end
+
+ unless File.size(file_fasta) == 0
+ prefix = File.join(options[:directory], "IDBA-UD")
+
+ commands = []
+ commands << "nice -n 19"
+ commands << "idba_ud"
+ commands << "--read #{file_fasta}"
+ commands << "--out #{prefix}"
+ commands << "--mink #{options[:kmer_min]}"
+ commands << "--maxk #{options[:kmer_max]}"
+ 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(" ")
+
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ file_contig = File.join(options[:directory], "IDBA-UD", "contig.fa")
+
+ Fasta.open(file_contig, "r") do |fasta_io|
+ fasta_io.each do |entry|
+ output.puts entry.to_bp
+ end
+ end
+ end
end
-output = [options[:directory], options[:name] ].join(File::SEPARATOR)
-
-commands = []
-commands << "nice -n 19"
-commands << "idba"
-commands << "--read #{file_fasta}"
-commands << "--output #{output}"
-commands << "--scaffold" if options[:scaffold]
-commands << "--mink #{options[:k_value_min]}"
-commands << "--maxk #{options[:k_value_max]}"
-commands << "--minCount #{options[:count_min]}"
-commands << "--cover #{options[:cover]}"
-commands << "--minPairs #{options[:pairs_min]}"
-commands << "--prefixLength #{options[:prefix_len]}"
-commands << "> /dev/null 2>&1" unless options[:verbose]
-
-command = commands.join(" ")
-system(command)
-raise "Command failed: #{command}" unless $?.success?
+FileUtils.remove_entry_secure file_fasta
+FileUtils.remove_entry_secure options[:directory] if options[:clean]
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
projects / biopieces.git / blobdiff