adding bzip2 support in ruby

[biopieces.git] / bp_bin / plot_phastcons_profiles

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..a72c46bf93a06a8b50136381bd3dcf4df4f581f2 100755 (executable)
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -1,6 +1,127 @@
 #!/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 chromosome distribution histogram.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+use Maasha::Matrix;
+use Maasha::Filesys;
+use Maasha::UCSC;
+use Maasha::UCSC::Wiggle;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
+     $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh, $tmp_dir );
+
+$default   = "PhastCons Profiles";
+$terminals = "dumb,x11,aqua,post,svg";
+
+$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 => 'file',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'genome',     short => 'g', type => 'genome', mandatory => 'yes', default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'mean',       short => 'm', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'median',     short => 'M', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'flank',      short => 'f', type => 'uint',   mandatory => 'no',  default => 0,        allowed => undef,      disallowed => undef },
+        { long => 'terminal',   short => 't', type => 'string', mandatory => 'no',  default => 'dumb',   allowed => $terminals, disallowed => undef },
+        { long => 'title',      short => 'T', type => 'string', mandatory => 'no',  default => $default, allowed => undef,      disallowed => undef },
+        { long => 'xlabel',     short => 'X', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'ylabel',     short => 'Y', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'logscale_y', short => 'L', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$phastcons_file  = Maasha::Config::genome_phastcons( $options->{ "genome" } );
+$phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
+
+$index           = Maasha::UCSC::Wiggle::fixedstep_index_retrieve( $phastcons_index );
+$fh_phastcons    = Maasha::Filesys::file_read_open( $phastcons_file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+    {
+        $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+                                                                               $record->{ "CHR_BEG" },
+                                                                               $record->{ "CHR_END" },
+                                                                               $options->{ "flank" } );
+
+        push @{ $AoA }, [ @{ $scores } ];
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+Maasha::UCSC::phastcons_normalize( $AoA );
+
+$AoA = [ [ Maasha::UCSC::phastcons_mean( $AoA ) ] ] if $options->{ "mean" };
+$AoA = [ [ Maasha::UCSC::phastcons_median( $AoA ) ] ] if $options->{ "median" };
+
+$AoA = Maasha::Matrix::matrix_flip( $AoA );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$plot = Maasha::Plot::lineplot_simple( $AoA, $options, $tmp_dir );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh "$_\n" foreach @{ $plot };
+
+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__