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 # Write sequence type records to FASTQ files according to a specified key.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fastq'
35 allowed_enc = 'base_33,base_64'
38 casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
39 casts << {:long=>'dir', :short=>'d', :type=>'dir!', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
40 casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
41 casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'base_33', :allowed=>allowed_enc, :disallowed=>nil}
43 options = Biopieces.options_parse(ARGV, casts)
45 encoding = options[:encoding].to_sym
47 key = options[:key].to_sym
51 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
52 input.each_record do |record|
53 if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES] and record[key]
54 entry = Seq.new_bp(record)
55 entry.qual_convert!(:base_33, encoding)
57 if fh_hash[record[key].to_sym]
58 fastq_io = fh_hash[record[key].to_sym]
60 fastq_file = File.join(options[:dir], record[key] + ".fastq")
61 fastq_io = Fastq.open(fastq_file, "w")
62 fh_hash[record[key].to_sym] = fastq_io
65 fastq_io.puts entry.to_fastq
68 output.puts record unless options[:no_stream]
72 fh_hash.each_value { |val| val.close }
74 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<