removed debug message

[biopieces.git] / bp_bin / rename_keys

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
deleted file mode 120000 (symlink)
index 78541e180885c73ffd9a5bad6405d0cd9ce8ba3a..0000000000000000000000000000000000000000
--- a/bp_bin/rename_keys
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/rename_keys
\ No newline at end of file

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..b0dc229a983f231d91c9406abc1538c8111aa055
--- /dev/null
+++ b/bp_bin/rename_keys
@@ -0,0 +1,82 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Rename keys of records in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', 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 ( exists $record->{ $options->{ "keys" }->[ 0 ] } )
+    {
+        $record->{ $options->{ "keys" }->[ 1 ] } = $record->{ $options->{ "keys" }->[ 0 ] };
+
+        delete $record->{ $options->{ "keys" }->[ 0 ] };
+    }
+
+    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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__