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
30 unique_genes_msa = Msa.new
31 longest_non_unique_genes_msa = Msa.new
33 fragment_re = /fragment/i
38 for i in 0 ... msa.get_number_of_seqs()
39 seq = msa.get_sequence( i )
41 if all_names.include?( name )
42 puts "error: " + name + " is not unique (#" + i + ")"
47 mol_seq = seq.get_sequence_as_string.upcase
48 if all_seqs.include?( mol_seq )
49 puts "error: sequence of " + name + " is not unique (#" + i + ")"
55 if fragment_re.match( name )
56 puts "ignored because fragment: " + name
61 gn_match = gn_re.match( name )
62 if IGNORE_SEQS_LACKING_GN
64 puts "ignored because no GN=: " + name
70 puts "no GN=: " + name
78 if IGNORE_SEQS_LACKING_GN
85 unless gn_to_seqs.has_key?(gn)
86 gn_to_seqs[gn] = Msa.new
88 gn_to_seqs[gn].add_sequence(seq)
91 puts "Sequences ignored because \"fragment\" in desc: " + frag_counter.to_s
92 puts "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s
97 gn_to_seqs.each_pair do |gene,seqs|
98 if seqs.get_number_of_seqs > 1
99 puts counter.to_s + ": " + gene
106 for j in 0 ... seqs.get_number_of_seqs()
107 current = seqs.get_sequence( j )
108 if current.get_length > longest
109 longest = current.get_length
110 longest_seq = current
113 longest_non_unique_genes_msa.add_sequence(longest_seq)
115 unique_genes_msa.add_sequence( seqs.get_sequence( 0 ) )
119 w.write(unique_genes_msa, "seqs_from_unique_genes.fasta")
120 w.write(longest_non_unique_genes_msa, "longest_seqs_from_nonunique_genes.fasta")