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 # Read Biopieces Genome Browser track into the stream.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
33 use Maasha::BGB::Track;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $user, $options, $in, $out, $record, $entry, @contigs, $contig, @tracks, $track, $fh );
42 $user = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
44 $options = Maasha::Biopieces::parse_options(
46 { long => 'user', short => 'u', type => 'string', mandatory => 'yes', 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 => 'track', short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
54 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
55 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
57 while ( $record = Maasha::Biopieces::get_record( $in ) )
59 Maasha::Biopieces::put_record( $record, $out );
62 Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
64 @contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
66 foreach $contig ( @contigs )
68 @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
70 foreach $track ( @tracks )
72 if ( ( index $track, $options->{ 'track' } ) >= 0 )
74 $fh = Maasha::Filesys::file_read_open( "$track/track_data.kiss" );
76 while ( $entry = Maasha::KISS::kiss_entry_get( $fh ) )
78 if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
79 Maasha::Biopieces::put_record( $record, $out );
88 Maasha::Biopieces::close_stream( $in );
89 Maasha::Biopieces::close_stream( $out );
92 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
97 Maasha::Biopieces::status_set();
103 Maasha::Biopieces::status_log();
107 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<