3 # Copyright (C) 2007-2009 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
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # Create a BWA index from sequences in stream for use with [bwa_seq].
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
38 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
41 my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry );
43 $options = Maasha::Biopieces::parse_options(
45 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
46 { long => 'directory', short => 'd', type => 'dir', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
47 { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
51 Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
53 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
54 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
56 $tmp_dir = Maasha::Biopieces::get_tmpdir();
57 $file_tmp = "$tmp_dir/create_bwa_index.seq";
58 $fh_tmp = Maasha::Filesys::file_write_open( $file_tmp );
60 while ( $record = Maasha::Biopieces::get_record( $in ) )
62 if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
63 Maasha::Fasta::put_entry( $entry, $fh_tmp );
66 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
71 Maasha::BWA::bwa_index( $file_tmp, $options->{ 'directory' }, $options->{ 'index_name' }, $options->{ 'verbose' } );
75 Maasha::Biopieces::close_stream( $in );
76 Maasha::Biopieces::close_stream( $out );
79 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
84 Maasha::Biopieces::status_set();
90 Maasha::Biopieces::status_log();
94 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<