3 # Copyright (C) 2007-2013 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 # Find SNPs in records of SAM type in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 require 'maasha/biopieces'
36 casts << {:long=>'coverage', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 options = Biopieces.options_parse(ARGV, casts)
40 snp_hash = Hash.new { |hash, key| hash[key] = Hash.new { |h, k| h[k] = Hash.new(0) } }
41 cov_hash = Hash.new { |hash, key| hash[key] = Hash.new(0) }
43 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
44 input.each_record do |record|
52 record[:ALIGN].split(',').each do |snp|
53 pos, event = snp.split(':')
55 pos = pos.to_i + record[:S_BEG].to_i
57 snp_hash[record[:S_ID].to_sym][pos][event.to_sym] += 1
61 if options[:coverage] and
65 (record[:S_BEG].to_i .. record[:S_END].to_i).each do |i|
66 cov_hash[record[:S_ID].to_sym][i] += 1
71 snp_hash.each_pair do |s_id, pos_hash|
73 new_record[:REC_TYPE] = 'SNP'
74 new_record[:S_ID] = s_id
76 pos_hash.each_pair do |pos, event_hash|
77 new_record[:POS] = pos
78 new_record[:COVERAGE] = cov_hash[s_id][pos] if options[:coverage]
80 event_hash.each_pair do |event, count|
81 new_record[:EVENT] = event
82 new_record[:SNP_COUNT] = count
84 before, after = event.to_s.split('>')
94 new_record[:TYPE] = type
97 output.puts new_record
102 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<