From 5280e3f844606335557d7535ed33ffd8174469fd Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 13 Jul 2012 14:15:39 +0000 Subject: [PATCH] fixed grave bug in find_orfs git-svn-id: http://biopieces.googlecode.com/svn/trunk@1870 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/find_orfs | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/bp_bin/find_orfs b/bp_bin/find_orfs index 868665d..a1203ea 100755 --- a/bp_bin/find_orfs +++ b/bp_bin/find_orfs @@ -37,12 +37,14 @@ casts << {:long=>'start_codons', :short=>'s', :type=>'list', :mandatory=>true, casts << {:long=>'stop_codons', :short=>'S', :type=>'list', :mandatory=>true, :default=>"UAA,UGA,UAG", :allowed=>nil, :disallowed=>nil} casts << {:long=>'min_size', :short=>'m', :type=>'uint', :mandatory=>true, :default=>50, :allowed=>nil, :disallowed=>'0'} casts << {:long=>'max_size', :short=>'M', :type=>'uint', :mandatory=>true, :default=>10_000, :allowed=>nil, :disallowed=>'0'} -casts << {:long=>'non_redundant', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'} +casts << {:long=>'non_redundant', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'} options = Biopieces.options_parse(ARGV, casts) Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| input.each_record do |record| + output.puts record + if record[:SEQ] entry = Seq.new_bp(record) @@ -55,11 +57,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| output.puts new_record end - - exit end - - output.puts record end end -- 2.39.5