in progress

[jalview.git] / forester / ruby / evoruby / exe / select_same_gn.rb

diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb
index 7ab2c91..275a149 100755 (executable)
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -29,19 +29,21 @@ module Evoruby
   fragment_re = /fragment/i
 
   frag_counter = 0
+  no_gn_counter = 0
 
   for i in 0 ... msa.get_number_of_seqs()
     seq = msa.get_sequence( i )
     name = seq.get_name
-
     if fragment_re.match( name )
+      puts "ignored because fragment: " + name
       frag_counter += 1
       next
     end
     gn_match = gn_re.match( name )
     unless gn_match
-      puts "no match in " + name
-      exit
+      puts "ignored because no GN=: " + name
+      no_gn_counter += 1
+      next
     end
     gn = gn_match[1]
     unless gn_to_seqs.has_key?(gn)
@@ -51,6 +53,7 @@ module Evoruby
   end
 
   puts "Sequeunces ignored because \"fragment\" in desc: " + frag_counter.to_s
+  puts "Sequeunces ignored because no \"GN=\" in desc  : " + no_gn_counter.to_s
   puts
   puts
 
@@ -77,6 +80,6 @@ module Evoruby
     end
   end
   w = FastaWriter.new
-  w.write(unique_genes_msa, "uniques.fasta")
-  w.write(longest_non_unique_genes_msa, "non_uniques_longest.fasta")
+  w.write(unique_genes_msa, "seqs_from_unique_genes.fasta")
+  w.write(longest_non_unique_genes_msa, "longest_seqs_from_nonunique_genes.fasta")
 end