adding bzip2 support in ruby

[biopieces.git] / bp_bin / sum_vals

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
deleted file mode 120000 (symlink)
index 4193a498fd428fe099c78abbafcd2a42e4a9ce62..0000000000000000000000000000000000000000
--- a/bp_bin/sum_vals
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/sum_vals
\ No newline at end of file

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..e20f178d504f4c65cf772a4283ea7a16b83978c8
--- /dev/null
+++ b/bp_bin/sum_vals
@@ -0,0 +1,108 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Calculate the total sums for the values of given keys.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Calc;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $new_record, $key, %sum_hash, $fh );
+
+$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" } } )
+    {
+        if ( $record->{ $key } ) {
+            $sum_hash{ $key } += $record->{ $key };
+        }
+    }
+
+    if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
+        $record->{ $options->{ 'list' } . "_SUM" } = sprintf( "%.2f", Maasha::Calc::sum( [ 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" } } ) {
+    $new_record->{ $key . "_SUM" } = $sum_hash{ $key } || 0;
+}
+
+if ( $options->{ "keys" } and $new_record )
+{
+    $new_record->{ 'REC_TYPE' } = "SUM";
+
+    Maasha::Biopieces::put_record( $new_record, $fh );
+}
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__