refactoring of assemble_pairs

[biopieces.git] / bp_bin / length_seq

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
index 4a9433383b85882a483cd8860c9663d32b864598..04384db3660c7762ccb1b99f9500d8a2e4bd3dc5 100755 (executable)
--- a/bp_bin/length_seq
+++ b/bp_bin/length_seq
@@ -1,6 +1,6 @@
-#!/usr/bin/env perl
+#!/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
@@ -18,63 +18,29 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Determines the length of all sequences in the stream as well as a total length.
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# This program is part of the Biopieces framework (www.biopieces.org).
 
-use strict;
-use Maasha::Biopieces;
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# Determines the length of each sequence in the stream.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $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 );
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
+require 'maasha/biopieces'
 
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
+casts = []
 
+options = Biopieces.options_parse(ARGV, casts)
 
-END
-{
-    Maasha::Biopieces::status_log();
-}
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    record[:SEQ_LEN] = record[:SEQ].length if record[:SEQ]
+    output.puts record
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<