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 # Find genes in prokaryotic genomic sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 require 'maasha/biopieces'
33 require 'maasha/fasta'
34 require 'maasha/prodigal'
37 casts << {:long=>'full', :short=>'f', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
38 casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true, :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
40 options = Biopieces.options_parse(ARGV, casts)
42 tmpdir = Biopieces.mktmpdir
43 infile = File.join(tmpdir, "in.fna")
44 outfile = File.join(tmpdir, "out.prodigal")
46 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
47 Fasta.open(infile, mode="w") do |fasta_io|
48 input.each_record do |record|
51 if record[:SEQ_NAME] and record[:SEQ]
52 seq = Seq.new_bp(record)
53 fasta_io.puts seq.to_fasta
58 prodigal = Prodigal.new(infile, outfile, options)
61 prodigal.each do |record|
62 record[:DEFINITION].match /seqhdr="([^"]+)/ do |m|
71 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<