in progress

[jalview.git] / forester / ruby / evoruby / lib / evo / apps / domains_to_forester.rb

diff --git a/forester/ruby/evoruby/lib/evo/apps/domains_to_forester.rb b/forester/ruby/evoruby/lib/evo/apps/domains_to_forester.rb
index a031150..85af666 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/apps/domains_to_forester.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/domains_to_forester.rb
@@ -56,6 +56,7 @@ module Evoruby
       File.open( domains_list_file ) do | file |
         while line = file.gets
           if !is_ignorable?( line )
+            
             a = line.split( column_delimiter )
             l = a.length
             if ( ( l < 4 ) || ( e_value_threshold >= 0.0 && l < 5 ) )
@@ -66,6 +67,14 @@ module Evoruby
             domain_name  = a[ 1 ]
             seq_from     = -1
             seq_to       = -1
+            ##########################################
+            if domain_name =~ /RRM_\d/
+              puts "ignoring " + line 
+              next
+            end
+            ##########################################
+            
+            
             begin
               seq_from = a[ 2 ].to_i
             rescue Exception
@@ -115,7 +124,7 @@ module Evoruby
         protein_name     = d[ 0 ]
         domain_structure = d[ 1 ]
         out.print( protein_name.to_s )
-        out.print( ":" )
+        out.print( ": " )
         out.print( domain_structure.to_NHX )
         out.print( Constants::LINE_DELIMITER  )
       end