From 3614bbf79718eed5617ff8d0072bf2aa047e0209 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 20 Jul 2012 21:41:15 +0000 Subject: [PATCH] linkers! --- .../evoruby/lib/evo/apps/multi_sequence_extractor.rb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb index 564e451..c97c0de 100644 --- a/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb @@ -150,10 +150,14 @@ module Evoruby puts( "Mapping file : " + mapping_file ) log << "Mapping file : " + mapping_file + ld end - if ( extension > 0 ) + if extension > 0 puts( "Extension : " + extension.to_s ) log << "Extension : " + extension.to_s + ld end + if extract_linkers + puts( "Extract linkers : true" ) + log << "Extract linkers : true" + ld + end log << "Date : " + Time.now.to_s + ld puts @@ -237,9 +241,9 @@ module Evoruby new_msa_domains_extended = Msa.new per_species_counter = 0 linkers = "" - + puts basename - + File.open( input_file ) do | file | while line = file.gets line.strip! @@ -436,7 +440,7 @@ module Evoruby rescue Exception => e Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end - + if extract_linkers begin f = File.open( out_dir + Constants::FILE_SEPARATOR + basename + LINKERS_SUFFIX , 'a' ) @@ -446,7 +450,7 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end end - + end -- 1.7.10.2