removed debug message

[biopieces.git] / bp_bin / compute

diff --git a/bp_bin/compute b/bp_bin/compute
index c8c800fbc01100b8cd9e82c26358933e470ca42e..0bcd6ca9fe6bea499411b1dc207bfcbc4a2bd64e 100755 (executable)
--- a/bp_bin/compute
+++ b/bp_bin/compute
@@ -1,6 +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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Performs computations on records in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $eval_key, @keys, $eval_val );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'eval',   short => 'e', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'format', short => 'f', type => 'string', mandatory => 'no',  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 ) ) 
+{
+    if ( $options->{ "eval" } =~ /^(\S+)\s*=\s*(.+)$/ )
+    {
+        $eval_key = $1;
+        $eval_val = $2;
+
+        if ( not @keys )
+        {
+            @keys = split /\s+|\+|-|\*|\/|\*\*/, $eval_val;
+
+            @keys = grep { exists $record->{ $_ } } @keys;
+        }
+
+        map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } @keys;
+
+        if ( $eval_val =~ /\+|\-|\*|\// or $eval_val =~ /\s+x\s+/)
+        {
+            $record->{ $eval_key } = eval "$eval_val";
+            Maasha::Common::error( qq(eval "$eval_key = $eval_val" failed -> $@) ) if $@;
+            $record->{ $eval_key } = sprintf( $options->{ 'format' }, $record->{ $eval_key } ) if $options->{ 'format' };
+        }
+        else
+        {
+            $record->{ $eval_key } = $eval_val;
+        }
+    }
+    else
+    {
+        Maasha::Common::error( qq(Bad compute expression: "$options->{ 'eval' }"\n) );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::Biotools;
+__END__