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 = 'base_33,base_64'
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: 'base_33', allowed: allowed_enc, disallowed: nil}
40 casts << {long: 'compress', short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
42 options = Biopieces.options_parse(ARGV, casts)
44 encoding = options[:encoding].to_sym
45 compress = options[:compress] ? options[:compress].to_sym : nil
47 raise "--data_out is mandatory for compressed output" if compress and not options[:data_out]
49 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
50 fastq_out = options[:data_out] ? Fastq.open(options[:data_out], 'w', compress: compress) : STDOUT
52 input.each do |record|
53 if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
54 entry = Seq.new_bp(record)
55 entry.qual_convert!(:base_33, encoding)
57 fastq_out.puts entry.to_fastq
60 output.puts record unless options[:no_stream]
67 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<