added BGB_list

[biopieces.git] / bp_bin / BGB_list

diff --git a/bp_bin/BGB_list b/bp_bin/BGB_list
new file mode 100755 (executable)
index 0000000..1cc1c0b
--- /dev/null
+++ b/bp_bin/BGB_list
@@ -0,0 +1,120 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# List all tracks availible in a local installation of the Biopieces Genome Browser.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::BGB::Common;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $user, $options, $in, $out, $record, $dir_hash, $clade, $genome, $assembly, $contig, $track );
+
+$user    = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'user', short => 'u', type => 'string', mandatory => 'yes', default => $user, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+
+foreach $clade ( Maasha::BGB::Common::list_clades( $options->{ 'user' } ) )
+{
+    foreach $genome ( Maasha::BGB::Common::list_genomes( $options->{ 'user' }, $clade ) )
+    {
+        foreach $assembly ( Maasha::BGB::Common::list_assemblies( $options->{ 'user' }, $clade, $genome ) )
+        {
+            foreach $contig ( Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $clade, $genome, $assembly ) )
+            {
+                foreach $track ( Maasha::BGB::Common::list_tracks( $options->{ 'user' }, $clade, $genome, $assembly, $contig ) ) {
+                    $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
+                }
+            }
+        }
+    }
+}
+
+foreach $clade ( keys %{ $dir_hash->{ $options->{ 'user' } } } )
+{
+    foreach $genome ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade } } )
+    {
+        foreach $assembly ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome } } )
+        {
+            foreach $track ( keys %{ $dir_hash->{ $options->{ 'user' } }->{ $clade }->{ $genome }->{ $assembly } } )
+            {
+                $record = {
+                    USER     => $options->{ 'user' },
+                    CLADE    => $clade,
+                    GENOME   => $genome,
+                    ASSEMBLY => $assembly,
+                    TRACK    => $track,
+                };
+
+                Maasha::Biopieces::put_record( $record, $out );
+            }
+        }
+    }
+}
+
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__