From ebbe2bae7f84efe52233f8c5cca06f4e71678eea Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 17 Dec 2009 17:40:07 +0000
Subject: [PATCH] added BGB_read_track

git-svn-id: http://biopieces.googlecode.com/svn/trunk@826 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/BGB_read_track | 110 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 110 insertions(+)
 create mode 100755 bp_bin/BGB_read_track

diff --git a/bp_bin/BGB_read_track b/bp_bin/BGB_read_track
new file mode 100755
index 0000000..ec468e1
--- /dev/null
+++ b/bp_bin/BGB_read_track
@@ -0,0 +1,110 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read Biopieces Genome Browser track into the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::BGB::Common;
+use Maasha::KISS;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $user, $options, $in, $out, $record, $entry, @contigs, $contig, @tracks, $track, $fh );
+
+$user    = Maasha::Biopieces::biopiecesrc( "BPB_USER" );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'user',     short => 'u', type => 'string', mandatory => 'yes', default => $user, allowed => undef, disallowed => undef },
+        { long => 'clade',    short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'genome',   short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'assembly', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'track',    short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$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();
+
+@contigs = Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+
+foreach $contig ( @contigs )
+{
+    @tracks = Maasha::BGB::Common::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
+
+    foreach $track ( @tracks )
+    {
+        if ( ( index $track, $options->{ 'track' } ) >= 0 )
+        {
+            $fh = Maasha::Filesys::file_read_open( "$track/track_data.kiss" );
+        
+            while ( $entry = Maasha::KISS::kiss_entry_get( $fh ) )
+            {
+                if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
+                    Maasha::Biopieces::put_record( $record, $out );
+                }
+            }
+
+            close $fh;
+        }
+    }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.5