From 411b46d576c5b42da1f3bb9bb61f20de2c104c72 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 7 Mar 2011 15:41:24 +0000 Subject: [PATCH] updated remove_illumina_adaptor git-svn-id: http://biopieces.googlecode.com/svn/trunk@1283 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/remove_illumina_adaptor | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/bp_bin/remove_illumina_adaptor b/bp_bin/remove_illumina_adaptor index ad52cc5..cb81799 100755 --- a/bp_bin/remove_illumina_adaptor +++ b/bp_bin/remove_illumina_adaptor @@ -33,8 +33,10 @@ require 'biopieces' require 'seq' casts = [] -casts << {:long=>'right', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} -casts << {:long=>'left', :short=>'l', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'right_adaptor', :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'left_adaptor', :short=>'l', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'right_hamming_dist', :short=>'R', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil} +casts << {:long=>'left_hamming_dist', :short=>'L', :type=>'uint', :mandatory=>false, :default=>25, :allowed=>nil, :disallowed=>nil} bp = Biopieces.new @@ -44,16 +46,16 @@ bp.each_record do |record| if record.has_key? :SEQ entry = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:TYPE], record[:SCORES]) - if options[:right] - pos_right = entry.adaptor_locate_right(options[:right]) + if options[:right_adaptor] + pos_right = entry.adaptor_locate_right(options[:right_adaptor], options[:right_hamming_dist]) entry.subseq!(0, pos_right) if pos_right >= 0 record[:CLIP_ADAPTOR_RIGHT] = pos_right else record[:CLIP_ADAPTOR_RIGHT] = -1 end - if options[:left] - pos_left = entry.adaptor_locate_left(options[:left]) + if options[:left_adaptor] + pos_left = entry.adaptor_locate_left(options[:left_adaptor], options[:left_hamming_dist]) entry.subseq!(pos_left + 1) if pos_left >= 0 record[:CLIP_ADAPTOR_LEFT] = pos_left else -- 2.39.5