From a56cf82543ada09c39c620ead6514e7c42f2bbfc Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 16 Jan 2013 02:56:03 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/exe/select_same_gn.rb | 34 +++++++++++++++++++++------ 1 file changed, 27 insertions(+), 7 deletions(-) diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb index 275a149..c27526a 100755 --- a/forester/ruby/evoruby/exe/select_same_gn.rb +++ b/forester/ruby/evoruby/exe/select_same_gn.rb @@ -12,6 +12,8 @@ module Evoruby input = ARGV[ 0 ] f = MsaFactory.new() + + IGNORE_SEQS_LACKING_GN = false msa = nil @@ -39,21 +41,39 @@ module Evoruby frag_counter += 1 next end + gn_match = gn_re.match( name ) - unless gn_match - puts "ignored because no GN=: " + name - no_gn_counter += 1 - next + if IGNORE_SEQS_LACKING_GN + unless gn_match + puts "ignored because no GN=: " + name + no_gn_counter += 1 + next + end + else + unless gn_match + puts "no GN=: " + name + end end - gn = gn_match[1] + + gn =nil + if gn_match + gn = gn_match[1] + else + if IGNORE_SEQS_LACKING_GN + puts "cannot be" + exit + end + gn = name + end + unless gn_to_seqs.has_key?(gn) gn_to_seqs[gn] = Msa.new end gn_to_seqs[gn].add_sequence(seq) end - puts "Sequeunces ignored because \"fragment\" in desc: " + frag_counter.to_s - puts "Sequeunces ignored because no \"GN=\" in desc : " + no_gn_counter.to_s + puts "Sequences ignored because \"fragment\" in desc: " + frag_counter.to_s + puts "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s puts puts -- 1.7.10.2