adding bzip2 support in ruby

[biopieces.git] / bp_bin / median_vals

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 4cd1d4413a253b7338666f848168a0f9929fba03..e32415ca05094bb872cf4d193c70fbae1e378a52 100755 (executable)
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -1,6 +1,112 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Find the median values in the stream for given keys.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
-
 use Maasha::Biopieces;
+use Maasha::Calc;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $new_record, $key, %median_hash, $median, $fh );
+
+$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 => 'keys',      short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'list',      short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qq(both --keys and --list specified) ) if     $options->{ "keys" } and     $options->{ "list" };
+Maasha::Common::error( qq(no --keys or --list specified) )    if not $options->{ "keys" } and not $options->{ "list" };
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    foreach $key ( @{ $options->{ "keys" } } ) {
+        push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
+    }
+
+    if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
+        $record->{ $options->{ 'list' } . "_MEDIAN" } = sprintf( "%.2f", Maasha::Calc::median( [ split ";", $record->{ $options->{ 'list' } } ] ) );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+foreach $key ( @{ $options->{ "keys" } } )
+{
+    if ( $median_hash{ $key } ) {
+        $median = Maasha::Calc::median( $median_hash{ $key } );
+    } else {
+        $median = "N/A";
+    }
+
+    $new_record->{ $key . "_MEDIAN" } = $median;
+}
+
+if ( $options->{ "keys" } and $new_record )
+{
+    $new_record->{ 'REC_TYPE' } = "MEDIAN";
+
+    Maasha::Biopieces::put_record( $new_record, $fh );
+}
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__