-#!/usr/bin/env perl -w
+#!/usr/bin/env ruby
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2010 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
# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Determines the length of all sequences in the stream as well as a total length.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use strict;
-use Maasha::Biopieces;
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# This program is part of the Biopieces framework (www.biopieces.org).
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $total );
-
-$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 },
- ]
-);
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- if ( $record->{ "SEQ" } )
- {
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
- $total += $record->{ "SEQ_LEN" };
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-}
-
-Maasha::Biopieces::put_record( { TOTAL_SEQ_LEN => $total }, $out );
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# Determines the length of each sequence in the stream.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-BEGIN
-{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
-}
+require 'maasha/biopieces'
+casts = []
-END
-{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
+options = Biopieces.options_parse(ARGV, casts)
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
-}
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ record[:SEQ_LEN] = record[:SEQ].length if record.has_key? :SEQ
+ output.puts record
+ end
+end
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
__END__
-