1 # Copyright (C) 2007-2013 Martin A. Hansen.
3 # This program is free software; you can redistribute it and/or
4 # modify it under the terms of the GNU General Public License
5 # as published by the Free Software Foundation; either version 2
6 # of the License, or (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program; if not, write to the Free Software
15 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
17 # http://www.gnu.org/copyleft/gpl.html
19 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
21 # This software is part of the Biopieces framework (www.biopieces.org).
23 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
26 def self.pair(entry1, entry2, options = {})
27 assemble = self.new(entry1, entry2, options)
31 def initialize(entry1, entry2, options)
35 @options[:mismatches_max] ||= 0
36 @options[:overlap_min] ||= 1
37 @options[:overlap_max] ||= entry1.length
38 @options[:overlap_max] = [@options[:overlap_max], entry1.length, entry2.length].min
42 overlap = @options[:overlap_max]
44 na_seq1 = NArray.to_na(@entry1.seq.downcase, "byte")
45 na_seq2 = NArray.to_na(@entry2.seq.downcase, "byte")
47 while overlap >= @options[:overlap_min]
48 hamming_dist = (na_seq1[-1 * overlap .. -1] ^ na_seq2[0 ... overlap]).count_true
50 if hamming_dist <= percent2real(overlap, @options[:mismatches_max])
51 merged = @entry1 + @entry2[overlap .. -1]
53 if @entry1.qual and @entry2.qual
54 qual1 = @entry1.qual[@entry1.length - overlap .. -1]
55 qual2 = @entry2.qual[0 ... overlap]
57 na_qual1 = NArray.to_na(qual1, "byte")
58 na_qual2 = NArray.to_na(qual2, "byte")
60 qual = ((na_qual1 + na_qual2) / 2).to_s
62 merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
63 merged.qual[@entry1.length - overlap ... @entry1.length] = qual
73 def percent2real(length, percent)
74 (length * percent * 0.01).round