From 36ea5e3d816a5afe5042c28ff0c07394575521f5 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 28 Nov 2013 03:39:44 +0000 Subject: [PATCH] inprogress --- .../evoruby/lib/evo/tool/multi_sequence_extractor.rb | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) 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 40b1211..932a6b4 100644 --- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb @@ -314,21 +314,6 @@ module Evoruby Util.fatal_error( PRG_NAME, "error: seq name \"" + seq_name + "\" not unique" ) end - # if current_msa.find_by_name_start( seq_name, true ).size > 0 - # begin - # seq = current_msa.get_by_name_start( seq_name, true ).copy - # rescue ArgumentError => e - # Util.fatal_error( PRG_NAME, "error: " + e.to_s ) - # end - # else - # # Not found, try finding by partial match. - # begin - # seq = current_msa.get_by_name( seq_name, true, true ) - # rescue ArgumentError => e - # Util.fatal_error( PRG_NAME, "error: " + e.to_s ) - # end - # end - normalized_id = per_species_counter.to_s( 16 ).upcase + "_" + current_species @@ -552,7 +537,7 @@ module Evoruby rescue Exception => e Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end - if @seqs <= 100000000 + if @seqs <= 500000 @file_to_msa[ input ] = msa @seqs += msa.get_number_of_seqs puts " total seqs in memory: " + @seqs.to_s -- 1.7.10.2