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 adaptors or parts thereof from sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
37 casts << {:long=>'adaptor', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>20, :allowed=>nil, :disallowed=>nil}
39 casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
40 casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
44 options = bp.parse(ARGV, casts)
46 bp.each_record do |record|
47 if record.has_key? :SEQ
48 entry = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:TYPE], record[:SCORES])
50 if match = entry.adaptor_find(options[:adaptor], options[:mismatches], options[:insertions], options[:deletions])
51 record[:POS] = match.pos
59 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<