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 # Find all matches between sequences in the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
35 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 my ( $options, $in, $out, $record, @entries, $results, $tmp_dir );
40 $options = Maasha::Biopieces::parse_options(
42 { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
43 { long => 'direction', short => 'd', type => 'string', mandatory => 'no', default => 'both', allowed => 'both,forward,reverse', disallowed => undef },
47 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
48 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
50 $tmp_dir = Maasha::Biopieces::get_tmpdir();
52 while ( $record = Maasha::Biopieces::get_record( $in ) )
54 if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
55 push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
58 Maasha::Biopieces::put_record( $record, $out );
63 $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $tmp_dir );
65 map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
69 $results = Maasha::Match::match_mummer( [ shift @entries ], \@entries, $options, $tmp_dir );
71 map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
74 Maasha::Biopieces::close_stream( $in );
75 Maasha::Biopieces::close_stream( $out );
78 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
83 Maasha::Biopieces::status_set();
89 Maasha::Biopieces::status_log();
93 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<