-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
+use Data::Dumper;
use Maasha::Biopieces;
use Maasha::UCSC::Wiggle;
$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 },
- { long => 'compress', short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'key', short => 'k', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'step', short => 's', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => undef },
+ { 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 },
+ { long => 'compress', short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record, $options->{ "key" }, $options->{ "step" } ) ) {
Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh );
}
close $fh;
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
BEGIN
{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
+ Maasha::Biopieces::status_set();
}
+
END
{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
-
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+ Maasha::Biopieces::status_log();
}