3 # Copyright (C) 2007-2012 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 # Write sequences from stream in FASTQ format.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fastq'
34 allowed_enc = 'sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
37 casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'data_out', :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
39 casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'illumina1.3', :allowed=>allowed_enc, :disallowed=>nil}
40 casts << {:long=>'compress', :short=>'Z', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
42 options = Biopieces.options_parse(ARGV, casts)
44 encoding = options[:encoding].downcase.delete('.')
46 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
49 io_out = Zlib::GzipWriter.open(options[:data_out])
51 io_out = Fastq.open(options[:data_out], 'w')
57 input.each do |record|
58 if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
59 entry = Seq.new_bp(record)
60 entry.convert_scores!('illumina13', encoding)
62 io_out.puts entry.to_fastq
65 output.puts record unless options.has_key? :no_stream
72 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<