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'
16 IGNORE_SEQS_LACKING_GN = false
21 msa = f.create_msa_from_file( input, FastaParser.new() )
23 puts "error: " + e.to_s
29 unique_genes_msa = Msa.new
30 longest_non_unique_genes_msa = Msa.new
32 fragment_re = /fragment/i
37 for i in 0 ... msa.get_number_of_seqs()
38 seq = msa.get_sequence( i )
40 if all_names.include?( name )
41 puts "error: " + name + " is not unique"
47 if fragment_re.match( name )
48 puts "ignored because fragment: " + name
53 gn_match = gn_re.match( name )
54 if IGNORE_SEQS_LACKING_GN
56 puts "ignored because no GN=: " + name
62 puts "no GN=: " + name
70 if IGNORE_SEQS_LACKING_GN
77 unless gn_to_seqs.has_key?(gn)
78 gn_to_seqs[gn] = Msa.new
80 gn_to_seqs[gn].add_sequence(seq)
83 puts "Sequences ignored because \"fragment\" in desc: " + frag_counter.to_s
84 puts "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s
89 gn_to_seqs.each_pair do |gene,seqs|
90 if seqs.get_number_of_seqs > 1
91 puts counter.to_s + ": " + gene
98 for j in 0 ... seqs.get_number_of_seqs()
99 current = seqs.get_sequence( j )
100 if current.get_length > longest
101 longest = current.get_length
102 longest_seq = current
105 longest_non_unique_genes_msa.add_sequence(longest_seq)
107 unique_genes_msa.add_sequence( seqs.get_sequence( 0 ) )
111 w.write(unique_genes_msa, "seqs_from_unique_genes.fasta")
112 w.write(longest_non_unique_genes_msa, "longest_seqs_from_nonunique_genes.fasta")