+
+ species = nil
+ if IGNORE_SPECIES || species_re.match( name )
+ unless IGNORE_SPECIES
+ species = species_re.match( name )[ 1 ]
+ else
+ species = "XXXXX"
+ end
+
+ unless all_seqs_per_species.has_key?( 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 )
+ outfile.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