inprogress

diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb
index 66d3540..de61eed 100755 (executable)
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -53,6 +53,7 @@ module Evoruby
       next
     end
 
+    species = nil
     if species_re.match( name )
       s_match = species_re.match( name )
       species = s_match[1]
@@ -70,7 +71,8 @@ module Evoruby
         all_seqs << mol_seq
       end
     else
-      puts "no species for: " + name
+      puts "error: no species for: " + name
+      exit
     end
 
     gn_match = gn_re.match( name )
@@ -88,7 +90,7 @@ module Evoruby
 
     gn =nil
     if gn_match
-      gn = gn_match[1]
+      gn = gn_match[1] + "_" + species
     else
       if IGNORE_SEQS_LACKING_GN
         puts "cannot be"

diff --git a/forester/ruby/evoruby/files/test/select_same_gn_test.fasta b/forester/ruby/evoruby/files/test/select_same_gn_test.fasta
index e42b0ff..1ef4efe 100644 (file)
--- a/forester/ruby/evoruby/files/test/select_same_gn_test.fasta
+++ b/forester/ruby/evoruby/files/test/select_same_gn_test.fasta
@@ -1,18 +1,18 @@
 >a GN=nmi [XENTR]
 MDTSM
->d GN=akap17a [XENTR]
+>b GN=akap17a [XENTR]
 MDT
->e [XENTR]
+>c [XENTR]
 MDTSMEM
->b GN=nmi [XENTR]
+>d GN=nmi [XENTR]
 MDTSMEMSRNP
->c GN=nmi [XENTR]
+>e GN=nmi [XENTR]
 MDTSSEM
->f isoform [XENTR]
+>f GN=nmi [DROME]
+MDTS
+>g isoform [XENTR]
 MDTSSEM
->f isoform [XENLA]
+>h isoform [DROME]
 MDTSSEM
->f2 isoform 2 [XENTR]
-MDTSSEM
->who are you
+>h isoform [XENTR]
 MDTSSEM