-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::UCSC::BED;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $bed_entry, $new_record );
+my ( $options, $in, $out, $fh, $record, $bed_entry, $new_record );
$options = Maasha::Biopieces::parse_options(
[
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
-
if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $options->{ 'cols' } ) ) {
Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $options->{ 'cols' }, $options->{ 'check' } );
}
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();
}