inprogress

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
index e4889ff..552a94c 100755 (executable)
--- 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 (file)
--- 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