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 # Delete Biopieces Genome Browser track.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
34 use Maasha::Biopieces;
35 use Maasha::BGB::Track;
38 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
41 my ( $user, $options, $in, $out, $record, $entry, @contigs, $contig, @tracks, $track );
43 $user = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
45 $options = Maasha::Biopieces::parse_options(
47 { long => 'user', short => 'u', type => 'string', mandatory => 'yes', default => $user, allowed => undef, disallowed => undef },
48 { long => 'clade', short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
49 { long => 'genome', short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
50 { long => 'assembly', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
51 { long => 'track', short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
55 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
56 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
58 while ( $record = Maasha::Biopieces::get_record( $in ) )
60 Maasha::Biopieces::put_record( $record, $out );
63 Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
65 @contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
67 foreach $contig ( @contigs )
69 @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
71 foreach $track ( @tracks )
73 if ( ( split "/", $track )[ -1 ] eq $options->{ 'track' } )
75 print STDERR "Deleting track: $track\n" if $options->{ 'verbose' };
77 Maasha::Filesys::dir_remove( $track );
82 Maasha::Biopieces::close_stream( $in );
83 Maasha::Biopieces::close_stream( $out );
86 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
91 Maasha::Biopieces::status_set();
97 Maasha::Biopieces::status_log();
101 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<