From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 16 Jan 2013 22:55:12 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=89a0bf45be7d28991571b0aa08af686e8b4652cf;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb
index 083a6a7..272595c 100755
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -25,12 +25,13 @@ module Evoruby
   end
 
   all_names = Set.new
-  all_seqs = Set.new
+  all_seqs_per_species = Hash.new
   gn_to_seqs = Hash.new
   unique_genes_msa = Msa.new
   longest_non_unique_genes_msa = Msa.new
   gn_re = /GN=(\S+)/
   fragment_re = /fragment/i
+  species_re = /\[([A-Z]{3,5})\]$/
 
   frag_counter = 0
   no_gn_counter = 0
@@ -44,19 +45,30 @@ module Evoruby
     else
       all_names << name
     end
-    mol_seq = seq.get_sequence_as_string.upcase
-    if all_seqs.include?( mol_seq )
-      puts "error: sequence of \"" + name + "\" is not unique (#" + i.to_s + ")"
-      exit
-    else
-      all_seqs << mol_seq
-    end
-
+    #mol_seq = seq.get_sequence_as_string.upcase
+    #if all_seqs.include?( mol_seq )
+    #  puts "error: sequence of \"" + name + "\" is not unique (#" + i.to_s + ")"
+    #  exit
+    #else
+    #  all_seqs << mol_seq
+    #end
+
+    
+    
     if fragment_re.match( name )
       puts "ignored because fragment: " + name
       frag_counter += 1
       next
     end
+    
+    species = nil
+    if species_re.match( name )
+      species = species_re[1]
+      puts species
+    else 
+       puts "no species for: " + name
+       exit
+    end
 
     gn_match = gn_re.match( name )
     if IGNORE_SEQS_LACKING_GN