3 # Copyright (C) 2007-2013 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 # Create bowtie2 index from sequences in the stream.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
32 require 'maasha/fasta'
35 casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
36 casts << {:long=>'directory', :short=>'d', :type=>'dir', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
37 casts << {:long=>'index_name', :short=>'i', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
39 options = Biopieces.options_parse(ARGV, casts)
41 unless File.directory? options[:directory]
42 Dir.mkdir options[:directory]
45 tmpdir = Biopieces.mktmpdir
46 tmpfile = File.join(tmpdir, "tmp.fna")
48 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
49 Fasta.open(tmpfile, "w") do |fasta_io|
50 input.each_record do |record|
51 output.puts record unless options[:no_stream]
53 if record[:SEQ_NAME] and record[:SEQ]
54 fasta_io.puts Seq.new_bp(record).to_fasta
61 cmd << "bowtie2-build"
62 cmd << "-q" unless options[:verbose]
64 cmd << File.join(options[:directory], options[:index_name])
68 $stderr.puts c if options[:verbose]
72 raise "Error: executing #{c}" unless $?.success?
75 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<