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 # Remove primers from sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
33 require 'maasha/biopieces'
35 require 'maasha/seq/backtrack'
40 casts << {:long=>'forward', :short=>'f', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
41 casts << {:long=>'reverse', :short=>'r', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
42 casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>2, :allowed=>nil, :disallowed=>nil}
43 casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>nil}
44 casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>nil}
46 options = Biopieces.options_parse(ARGV, casts)
48 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
49 input.each do |record|
53 seq = Seq.new_bp(record)
55 seq.patscan(options[:forward].to_s, 0, options[:mismatches], options[:insertions], options[:deletions]) do |match|
56 record[:FORWARD_POS] = match.pos
57 record[:FORWARD_LEN] = match.length
58 pos = match.pos + match.length
59 len = seq.length - pos
60 seq.subseq!(pos, len) if len > 0
65 seq.patscan(options[:reverse].to_s, 0, options[:mismatches], options[:insertions], options[:deletions]) do |match|
66 record[:REVERSE_POS] = match.pos
67 record[:REVERSE_LEN] = match.length
73 seq.qual = "" if seq.qual
83 record.merge!(seq.to_bp)
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<