3 # Copyright (C) 2007-2011 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Assemble sequences in the stream using IDBA.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
35 casts << {:long=>'name', :short=>'n', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
36 casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
37 casts << {:long=>'scaffold', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'kmer_min', :short=>'k', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil}
39 casts << {:long=>'kmer_max', :short=>'K', :type=>'uint', :mandatory=>false, :default=>50, :allowed=>nil, :disallowed=>nil}
40 casts << {:long=>'count_min', :short=>'c', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
41 casts << {:long=>'cover', :short=>'C', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil}
42 casts << {:long=>'pairs_min', :short=>'p', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
43 casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3, :allowed=>nil, :disallowed=>nil}
44 casts << {:long=>'clean', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
48 options = bp.parse(ARGV, casts)
50 Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
52 file_fasta = [options[:directory], options[:name] ].join(File::SEPARATOR) + ".fna"
54 Fasta.open(file_fasta, mode="w") do |fasta_io|
55 bp.each_record do |record|
60 unless File.size(file_fasta) == 0
61 output = [options[:directory], options[:name] ].join(File::SEPARATOR)
64 commands << "nice -n 19"
66 commands << "--read #{file_fasta}"
67 commands << "--output #{output}"
68 commands << "--scaffold" if options[:scaffold]
69 commands << "--mink #{options[:kmer_min]}"
70 commands << "--maxk #{options[:kmer_max]}"
71 commands << "--minCount #{options[:count_min]}"
72 commands << "--cover #{options[:cover]}"
73 commands << "--minPairs #{options[:pairs_min]}"
74 commands << "--prefixLength #{options[:prefix_len]}"
75 commands << "> /dev/null 2>&1" unless options[:verbose]
77 command = commands.join(" ")
79 raise "Command failed: #{command}" unless $?.success?
81 file_contig = [options[:directory], options[:name] ].join(File::SEPARATOR) + "-contig.fa"
83 Fasta.open(file_contig, mode="r") do |fasta_io|
84 fasta_io.each do |entry|
90 FileUtils.remove_entry_secure options[:directory] if options[:clean]
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<