3 # Copyright (C) 2007-2010 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 sequences in the stream at a given restriction enzyme's cleavage points.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
35 casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
36 casts << {:long=>'cut_pos', :short=>'c', :type=>'int', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 options = Biopieces.options_parse(ARGV, casts)
40 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
41 input.each_record do |record|
42 if record[:SEQ_NAME] and record[:SEQ]
43 seq = Seq.new_bp(record)
45 seq.each_digest(options[:pattern].to_s, options[:cut_pos]) do |digest|
46 new_record = digest.to_bp
48 if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
53 new_record[:S_BEG] = s_beg
54 new_record[:S_END] = s_end
55 new_record[:REC_TYPE] = "DIGEST"
57 output.puts new_record
65 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<