refactoring of assemble_pairs

[biopieces.git] / bp_bin / plot_karyogram

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..2e3748be5a113282cc3997c8862744cbe19d137d 100755 (executable)
--- a/bp_bin/plot_karyogram
+++ b/bp_bin/plot_karyogram
@@ -1,6 +1,95 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Plot a karyogram with positions indicated according to records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, @data, $fh, $result, %data_hash );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef,   allowed => undef,      disallowed => undef },
+        { long => 'data_out',   short => 'o', type => 'string', mandatory => 'no',  default => undef,   allowed => undef,      disallowed => undef },
+        { long => 'genome',     short => 'g', type => 'string', mandatory => 'yes', default => undef,   allowed => 'hg18,mm9', disallowed => undef },
+        { long => 'feat_color', short => 'f', type => 'string', mandatory => 'no',  default => 'black', allowed => undef,      disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$options->{ "genome" }     ||= "human";
+$options->{ "feat_color" } ||= "black";
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+    {
+        push @{ $data_hash{ $record->{ "CHR" } } }, [ $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "feat_color" } ];
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+$result = Maasha::Plot::karyogram( \%data_hash, $options );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh $result;
+
+close $fh;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__