+++ /dev/null
-#!/usr/bin/env ruby
-
-# 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 program is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Assemble sequences in the stream using IDBA.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'maasha/biopieces'
-require 'maasha/fasta'
-
-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=>'metagenome', :short=>'m', :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=>'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=>'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"
-
-count = 0
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- Fasta.open(file_fasta, mode="w") do |fasta_io|
- input.each_record do |record|
- if record[:SEQ_NAME] and record[:SEQ]
- seq = Seq.new_bp(record)
-
- if options[:scaffold] # we need to fix the sequence name for mate-pair IDBA
- if seq.seq_name =~ /1$/
- seq.seq_name = "read#{count}/1"
- else
- seq.seq_name = "read#{count}/2"
-
- count += 1
- end
- end
-
- fasta_io.puts seq.to_fasta
- end
- end
- end
-
- unless File.size(file_fasta) == 0
- prefix = File.join(options[:directory], "IDBA")
-
- commands = []
- commands << "nice -n 19"
-
- if options[:metagenome]
- commands << "metaidba"
- else
- commands << "idba"
- end
-
- commands << "--read #{file_fasta}"
- commands << "--output #{prefix}"
- commands << "--scaffold" if options[:scaffold]
- 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 << "> /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
-
- if options[:scaffold]
- file_contig = File.join(options[:directory], "IDBA") + "-contig-mate.fa"
- else
- file_contig = File.join(options[:directory], "IDBA") + "-contig.fa"
- end
-
- Fasta.open(file_contig, mode="r") do |fasta_io|
- fasta_io.each do |entry|
- output.puts entry.to_bp
- end
- end
- end
-end
-
-FileUtils.remove_entry_secure file_fasta
-FileUtils.remove_entry_secure options[:directory] if options[:clean]
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__