inprogress

[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 c27526a..de61eed 100755 (executable)
--- a/forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/forester/ruby/evoruby/exe/select_same_gn.rb
@@ -12,7 +12,7 @@ module Evoruby
 
   input = ARGV[ 0 ]
   f = MsaFactory.new()
-  
+
   IGNORE_SEQS_LACKING_GN = false
 
   msa = nil
@@ -24,24 +24,57 @@ module Evoruby
     exit
   end
 
+  all_names = 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 = /\[([A-Z0-9]{3,6})\]$/
 
   frag_counter = 0
   no_gn_counter = 0
+  same_seq_counter = 0
 
   for i in 0 ... msa.get_number_of_seqs()
     seq = msa.get_sequence( i )
     name = seq.get_name
+    if all_names.include?( name )
+      puts "error: sequence name \"" + name + "\" is not unique (#" + i.to_s + ")"
+      exit
+    else
+      all_names << name
+    end
+
     if fragment_re.match( name )
       puts "ignored because fragment: " + name
       frag_counter += 1
       next
     end
-    
+
+    species = nil
+    if species_re.match( name )
+      s_match = species_re.match( name )
+      species = s_match[1]
+
+      unless all_seqs_per_species.include?( species )
+        all_seqs_per_species[ species ] = Set.new
+      end
+      all_seqs = all_seqs_per_species[ species ]
+      mol_seq = seq.get_sequence_as_string.upcase
+      if all_seqs.include?( mol_seq )
+        puts "ignored because identical sequence in same species: " + name
+        same_seq_counter += 1
+        next
+      else
+        all_seqs << mol_seq
+      end
+    else
+      puts "error: no species for: " + name
+      exit
+    end
+
     gn_match = gn_re.match( name )
     if IGNORE_SEQS_LACKING_GN
       unless gn_match
@@ -54,26 +87,29 @@ module Evoruby
         puts "no GN=: " + name
       end
     end
-    
+
     gn =nil
     if gn_match
-      gn = gn_match[1]
+      gn = gn_match[1] + "_" + species
     else
       if IGNORE_SEQS_LACKING_GN
         puts "cannot be"
         exit
       end
       gn = name
-    end  
-    
+    end
+
     unless gn_to_seqs.has_key?(gn)
       gn_to_seqs[gn] = Msa.new
     end
     gn_to_seqs[gn].add_sequence(seq)
   end
 
-  puts "Sequences ignored because \"fragment\" in desc: " + frag_counter.to_s
-  puts "Sequences ignored because no \"GN=\" in desc  : " + no_gn_counter.to_s
+  puts "Sequences ignored because \"fragment\" in desc                : " + frag_counter.to_s
+  if IGNORE_SEQS_LACKING_GN
+    puts "Sequences ignored because no \"GN=\" in desc                  : " + no_gn_counter.to_s
+  end
+  puts "Sequences ignored because identical sequence in same species: " + same_seq_counter.to_s
   puts
   puts