From b35ac7de74589875baabdd2f7b5fe8d5cd43ab33 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 30 Jan 2015 23:46:58 +0000 Subject: [PATCH] can turn off ignore frag now --- forester/ruby/evoruby/exe/select_same_gn.rb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb index 8fcb6be..7dbe9f1 100755 --- a/forester/ruby/evoruby/exe/select_same_gn.rb +++ b/forester/ruby/evoruby/exe/select_same_gn.rb @@ -19,6 +19,7 @@ module Evoruby f = MsaFactory.new() IGNORE_SEQS_LACKING_GN = false + IGNORE_FRAGMENTS = false IGNORE_SPECIES = true msa = nil @@ -58,8 +59,7 @@ module Evoruby all_names << name end - if fragment_re.match( name ) - + if IGNORE_FRAGMENTS && fragment_re.match( name ) outfile.puts("ignored because fragment: " + name) frag_counter += 1 next @@ -121,7 +121,10 @@ module Evoruby gn_to_seqs[gn].add_sequence(seq) end - outfile.puts( "Sequences ignored because \"fragment\" in desc : " + frag_counter.to_s ) + if IGNORE_FRAGMENTS + outfile.puts( "Sequences ignored because \"fragment\" in desc : " + frag_counter.to_s ) + end + if IGNORE_SEQS_LACKING_GN outfile.puts( "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s ) end -- 1.7.10.2