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 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 require 'maasha/biopieces'
33 require 'maasha/fasta'
37 casts << {:long=>'pattern', :short=>'p', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'cut_pos', :short=>'c', :type=>'int', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
40 options = Biopieces.options_parse(ARGV, casts)
42 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
43 input.each_record do |record|
44 if record.has_key? :SEQ_NAME and record.has_key? :SEQ
45 seq = Seq.new(record[:SEQ_NAME], record[:SEQ])
46 digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
48 digest.each do |subseq|
49 new_record = subseq.to_bp
51 if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
56 new_record[:S_BEG] = s_beg
57 new_record[:S_END] = s_end
58 new_record[:REC_TYPE] = "DIGEST"
59 output.puts new_record
68 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<