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
28 all_seqs_per_species = Hash.new
30 unique_genes_msa = Msa.new
31 longest_non_unique_genes_msa = Msa.new
33 fragment_re = /fragment/i
34 species_re = /\[([A-Z0-9]{3,6})\]$/
40 for i in 0 ... msa.get_number_of_seqs()
41 seq = msa.get_sequence( i )
43 if all_names.include?( name )
44 puts "error: sequence name \"" + name + "\" is not unique (#" + i.to_s + ")"
50 if fragment_re.match( name )
51 puts "ignored because fragment: " + name
57 if species_re.match( name )
58 s_match = species_re.match( name )
61 unless all_seqs_per_species.include?( species )
62 all_seqs_per_species[ species ] = Set.new
64 all_seqs = all_seqs_per_species[ species ]
65 mol_seq = seq.get_sequence_as_string.upcase
66 if all_seqs.include?( mol_seq )
67 puts "ignored because identical sequence in same species: " + name
74 puts "error: no species for: " + name
78 gn_match = gn_re.match( name )
79 if IGNORE_SEQS_LACKING_GN
81 puts "ignored because no GN=: " + name
87 puts "no GN=: " + name
93 gn = gn_match[1] + "_" + species
95 if IGNORE_SEQS_LACKING_GN
102 unless gn_to_seqs.has_key?(gn)
103 gn_to_seqs[gn] = Msa.new
105 gn_to_seqs[gn].add_sequence(seq)
108 puts "Sequences ignored because \"fragment\" in desc : " + frag_counter.to_s
109 if IGNORE_SEQS_LACKING_GN
110 puts "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s
112 puts "Sequences ignored because identical sequence in same species: " + same_seq_counter.to_s
117 gn_to_seqs.each_pair do |gene,seqs|
118 if seqs.get_number_of_seqs > 1
119 puts counter.to_s + ": " + gene
126 for j in 0 ... seqs.get_number_of_seqs()
127 current = seqs.get_sequence( j )
128 if current.get_length > longest
129 longest = current.get_length
130 longest_seq = current
133 longest_non_unique_genes_msa.add_sequence(longest_seq)
135 unique_genes_msa.add_sequence( seqs.get_sequence( 0 ) )
139 w.write(unique_genes_msa, "seqs_from_unique_genes.fasta")
140 w.write(longest_non_unique_genes_msa, "longest_seqs_from_nonunique_genes.fasta")