From 1403698a3e03de23438df8287ed08f2b2606fb7b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 3 Apr 2013 00:59:13 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/exe/run_phylo_pipeline.rb | 2 +- forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb index e4889ff..552a94c 100755 --- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb +++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb @@ -70,7 +70,7 @@ module Evoruby puts puts "4. dsx:" - cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}_#{hmm}_ee#{e_value_exp.to_s}_#{length}" + cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}__#{hmm}__ee#{e_value_exp.to_s}_#{length}" run_command( cmd ) puts diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb index 624623a..5e175f7 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogeny_factory.rb @@ -258,8 +258,9 @@ module Evoruby def get_id( aln_name ) id = nil - if aln_name.include? "__" - id = aln_name[ 0, aln_name.index( "__" ) ] + aln_name.index + if aln_name =~ /_{2}(.+)_{2}/ + id = $1 end id end -- 1.7.10.2