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 # List all tracks availible in a local installation of the Biopieces Genome Browser.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
33 use Maasha::BGB::Track;
36 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
39 my ( $user, $options, $in, $out, $record, $dir_hash, $clade, $genome, $assembly, $contig, $track );
41 $user = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
43 $options = Maasha::Biopieces::parse_options(
45 { long => 'user', short => 'u', type => 'string', mandatory => 'yes', default => $user, allowed => undef, disallowed => undef },
49 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
50 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
52 while ( $record = Maasha::Biopieces::get_record( $in ) )
54 Maasha::Biopieces::put_record( $record, $out );
57 Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
59 foreach $clade ( Maasha::BGB::Track::list_clades( $options->{ 'user' } ) )
61 foreach $genome ( Maasha::BGB::Track::list_genomes( $options->{ 'user' }, $clade ) )
63 foreach $assembly ( Maasha::BGB::Track::list_assemblies( $options->{ 'user' }, $clade, $genome ) )
65 foreach $contig ( Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $clade, $genome, $assembly ) )
67 foreach $track ( Maasha::BGB::Track::list_tracks( $options->{ 'user' }, $clade, $genome, $assembly, $contig ) ) {
68 $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
75 foreach $clade ( keys %{ $dir_hash->{ $options->{ 'user' } } } )
77 foreach $genome ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade } } )
79 foreach $assembly ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome } } )
81 foreach $track ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly } } )
84 USER => $options->{ 'user' },
87 ASSEMBLY => $assembly,
91 Maasha::Biopieces::put_record( $record, $out );
98 Maasha::Biopieces::close_stream( $in );
99 Maasha::Biopieces::close_stream( $out );
102 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
107 Maasha::Biopieces::status_set();
113 Maasha::Biopieces::status_log();
117 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<