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 # Read FASTQ entries from one or more files.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fastq'
34 allowed_enc = 'auto,sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
37 casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
39 casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'auto', :allowed=>allowed_enc, :disallowed=>nil}
41 options = Biopieces.options_parse(ARGV, casts)
46 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
47 unless options[:data_in] and options[:data_in].first == '-'
48 input.each_record do |record|
54 options[:data_in].each do |file|
55 encoding = options[:encoding].downcase.delete('.')
57 Fastq.open(file, mode='r') do |fastq|
60 if entry.qual_base33? # sanger or illumina18
61 encoding = 'illumina18'
62 elsif entry.qual_base64? # solexa or illumina13 or illumina15
63 encoding = 'illumina13'
65 raise SeqError, "Could not auto-detect quality score encoding"
69 entry.convert_scores!(encoding, 'illumina13')
70 output.puts entry.to_bp
73 if options[:num] == num
86 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<