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 # Intersects two tracks in the Biopieces Genome Browser.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
33 use Maasha::BGB::Track;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $user, $options, $in, $out, $record, @contigs, $contig, $track, @tracks, %hash, $fh1, $fh2, $entries, $entry );
42 $user = Maasha::Biopieces::biopiecesrc( "BGB_USER" );
44 $options = Maasha::Biopieces::parse_options(
46 { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => $user, allowed => undef, disallowed => undef },
47 { long => 'clade', short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
48 { long => 'genome', short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
49 { long => 'assembly', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
50 { long => 'track1', short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
51 { long => 'track2', short => 'T', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
52 { long => 'invert', short => 'i', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
56 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
57 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
59 while ( $record = Maasha::Biopieces::get_record( $in ) )
61 Maasha::Biopieces::put_record( $record, $out );
64 Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
66 @contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
68 foreach $contig ( @contigs )
72 @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
74 foreach $track ( @tracks )
76 if ( index( $track, $options->{ 'track1' } ) >= 0 ) {
77 $hash{ '1' } = $track;
78 } elsif ( index( $track, $options->{ 'track2' } ) >= 0 ) {
79 $hash{ '2' } = $track;
83 if ( exists $hash{ '1' } and exists $hash{ '2' } )
85 print STDERR "Intersecting:\n$hash{ '1' } and\n$hash{ '2' }\n\n" if $options->{ 'verbose' };
87 $fh1 = Maasha::Filesys::file_read_open( "$hash{ '1' }/track_data.kiss" );
88 $fh2 = Maasha::Filesys::file_read_open( "$hash{ '2' }/track_data.kiss" );
90 $entries = Maasha::KISS::kiss_intersect( $fh1, $fh2, $options->{ 'invert' } );
92 foreach $entry ( @{ $entries } )
94 if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
95 Maasha::Biopieces::put_record( $record, $out );
101 Maasha::Biopieces::close_stream( $in );
102 Maasha::Biopieces::close_stream( $out );
105 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
110 Maasha::Biopieces::status_set();
116 Maasha::Biopieces::status_log();
120 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<