3 # Copyright (C) 2007-2011 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Write sequence type records to FASTA files according to a specified key.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fasta'
36 casts << {long: 'key', short: 'k', type: 'string', mandatory: true, default: nil, allowed: nil, disallowed: nil}
37 casts << {long: 'dir', short: 'd', type: 'dir!', mandatory: true, default: nil, allowed: nil, disallowed: nil}
38 casts << {long: 'prefix', short: 'p', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
39 casts << {long: 'wrap', short: 'w', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
40 casts << {long: 'compress', short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
41 casts << {long: 'no_stream', short: 'x', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
43 options = Biopieces.options_parse(ARGV, casts)
45 key = options[:key].to_sym
46 compress = options[:compress] ? options[:compress].to_sym : nil
49 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
50 input.each_record do |record|
51 if record[:SEQ_NAME] and record[:SEQ] and record[key]
52 seq = Seq.new_bp(record)
54 if fh_hash[record[key].to_sym]
55 fasta_io = fh_hash[record[key].to_sym]
58 fasta_file = File.join(options[:dir], [options[:prefix], record[key]].join("_") + ".fasta")
60 fasta_file = File.join(options[:dir], record[key] + ".fasta")
63 fasta_file << ".gz" if compress == :gzip
64 fasta_file << ".bz2" if compress == :bzip or compress == :bzip2
65 fasta_io = Fasta.open(fasta_file, "w", compress: compress)
66 fh_hash[record[key].to_sym] = fasta_io
69 fasta_io.puts seq.to_fasta(options[:wrap])
72 output.puts record unless options[:no_stream]
76 fh_hash.each_value { |val| val.close }
78 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<