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 # Trim sequence ends removing residues with a low quality score.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
36 casts << {:long=>'min_qual', :short=>'m', :type=>'uint', :mandatory=>true, :default=>20, :allowed=>nil, :disallowed=>'0'}
37 casts << {:long=>'min_len', :short=>'l', :type=>'uint', :mandatory=>true, :default=>3, :allowed=>nil, :disallowed=>'0'}
38 casts << {:long=>'trim', :short=>'t', :type=>'string', :mandatory=>true, :default=>'both', :allowed=>'left,right,both', :disallowed=>nil}
40 options = Biopieces.options_parse(ARGV, casts)
42 trim = options[:trim].to_sym
44 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
45 input.each_record do |record|
46 if record[:SEQ] and record[:SCORES]
47 entry = Seq.new_bp(record)
50 when :both then entry.quality_trim!(options[:min_qual], options[:min_len])
51 when :left then entry.quality_trim_left!(options[:min_qual], options[:min_len])
52 when :right then entry.quality_trim_right!(options[:min_qual], options[:min_len])
55 record.merge! entry.to_bp
63 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<