adding bzip2 support in ruby

[biopieces.git] / bp_bin / add_ident

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
deleted file mode 120000 (symlink)
index f5577548abf4ab72bd7d983e77b640f3a2323296..0000000000000000000000000000000000000000
--- a/bp_bin/add_ident
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/add_ident
\ No newline at end of file

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..b15a86dbf7d6aa63f117574b36f756ca2a8c1e38
--- /dev/null
+++ b/bp_bin/add_ident
@@ -0,0 +1,86 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Add a unique identifier to each record in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $key, $prefix, $i );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',    short => 'k', type => 'string', mandatory => 'no', default => 'ID', allowed => undef, disallowed => undef },
+        { long => 'prefix', short => 'p', type => 'string', mandatory => 'no', default => 'ID', allowed => undef, disallowed => undef },
+        { long => 'offset', short => 'o', type => 'uint',   mandatory => 'no', default => '0',  allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$key    = $options->{ "key" };
+$prefix = $options->{ "prefix" };
+
+$i = $options->{ "offset" };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    $record->{ $key } = sprintf( "$prefix%08d", $i );
+
+    Maasha::Biopieces::put_record( $record, $out );
+
+    $i++;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__