3 # Copyright (C) 2007-2013 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 # Split joined pair-end sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
35 options = Biopieces.options_parse(ARGV)
37 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
38 input.each_record do |record|
39 if record[:SEQ_NAME] and record[:SEQ] and record[:SEQ_LEN_LEFT] and record[:SEQ_LEN_RIGHT]
40 entry = Seq.new_bp(record)
42 len_left = record[:SEQ_LEN_LEFT].to_i
43 len_right = record[:SEQ_LEN_RIGHT].to_i
45 unless len_left + len_right == entry.length
46 raise "SEQ_LEN_LEFT + SEQ_LEN_RIGHT != SEQ_LEN #{len_left} + #{len_right} != #{entry.length}"
49 entry1 = entry.subseq(0, len_left)
50 entry2 = entry.subseq(len_left)
52 if entry.seq_name =~ /^[^ ]+ \d:/
53 entry2.seq_name.sub!(/ \d:/, " 2:")
54 elsif entry.seq_name =~ /^.+\/\d$/
55 entry2.seq_name[-1] = "2"
57 raise "Could not match sequence name: #{entry.seq_name}"
60 output.puts entry1.to_bp
61 output.puts entry2.to_bp
69 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<