From: cmzmasek@gmail.com Date: Thu, 28 Nov 2013 01:08:39 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bc7e61297dc69bfe515f83a49e469ed7f5093518;p=jalview.git inprogress --- diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb index b435566..de143bc 100644 --- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb @@ -249,6 +249,7 @@ module Evoruby puts basename File.open( input_file ) do | file | + species_counter = 1 while line = file.gets line.strip! if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) @@ -290,8 +291,9 @@ module Evoruby print_counts( per_species_counter, log, Constants::LINE_DELIMITER ) per_species_counter = 0 end - puts " " + current_species + " [" + my_readlink + "]" - log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER + puts " " + species_counter.to_str + ": " + current_species + " [" + my_readlink + "]" + log << species_counter.to_str + ": " + current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER + species_counter += 1 end puts " " + seq_name log << " " + seq_name + Constants::LINE_DELIMITER