1 #!/usr/local/bin/ruby -w
4 require 'lib/evo/sequence/sequence'
5 require 'lib/evo/msa/msa'
6 require 'lib/evo/msa/msa_factory'
7 require 'lib/evo/io/writer/fasta_writer'
8 require 'lib/evo/io/parser/fasta_parser'
19 msa = f.create_msa_from_file( input, FastaParser.new() )
21 puts "error: " + e.to_s
26 unique_genes_msa = Msa.new
27 longest_non_unique_genes_msa = Msa.new
29 fragment_re = /fragment/i
34 for i in 0 ... msa.get_number_of_seqs()
35 seq = msa.get_sequence( i )
37 if fragment_re.match( name )
38 puts "ignored because fragment: " + name
42 gn_match = gn_re.match( name )
44 puts "ignored because no GN=: " + name
49 unless gn_to_seqs.has_key?(gn)
50 gn_to_seqs[gn] = Msa.new
52 gn_to_seqs[gn].add_sequence(seq)
55 puts "Sequeunces ignored because \"fragment\" in desc: " + frag_counter.to_s
56 puts "Sequeunces ignored because no \"GN=\" in desc : " + no_gn_counter.to_s
61 gn_to_seqs.each_pair do |gene,seqs|
62 if seqs.get_number_of_seqs > 1
63 puts counter.to_s + ": " + gene
70 for j in 0 ... seqs.get_number_of_seqs()
71 current = seqs.get_sequence( j )
72 if current.get_length > longest
73 longest = current.get_length
77 longest_non_unique_genes_msa.add_sequence(longest_seq)
79 unique_genes_msa.add_sequence( seqs.get_sequence( 0 ) )
83 w.write(unique_genes_msa, "seqs_from_unique_genes.fasta")
84 w.write(longest_non_unique_genes_msa, "longest_seqs_from_nonunique_genes.fasta")