From: cmzmasek@gmail.com Date: Wed, 4 Dec 2013 22:15:16 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e5dd11703745ff5693d9391537abbe69be45b4d3;p=jalview.git inprogress --- diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb index 795aba7..0808257 100644 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb @@ -135,12 +135,12 @@ module Evoruby dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" - unless File.exist? dsx_output + unless File.exist? dsx_output + ".fasta" puts "e. dsx:" cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmmscan_output} #{input} #{dsx_output}" run_command( cmd ) else - puts "e. dsx output already exists: " + dsx_output + puts "e. dsx output already exists: " + dsx_output + ".fasta" end puts @@ -163,12 +163,12 @@ module Evoruby run_1 = false run_100 = false - unless File.exist? "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" + unless File.exist? "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta" run_1 = true FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" end - unless File.exist? "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" + unless File.exist? "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta" run_100 = true FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}" end