+
+ 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 "no species for: " + name
+ end
+