-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Common;
use Maasha::Biopieces;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
+my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
$options = Maasha::Biopieces::parse_options(
[
close $fh_out;
if ( $format eq "BED" ) {
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+ Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
} elsif ( $format eq "PSL" ) {
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ Maasha::UCSC::BED::psl_upload_to_ucsc( $file, $options, $append );
}
unlink $file;
{
$type = "bed $columns";
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+ Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
}
elsif ( $format eq "BED_SS" )
{
$type = "type bed 6 +";
- Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+ Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
}
elsif ( $format eq "PSL" )
{
$type = "psl";
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ Maasha::UCSC::PSL::psl_upload_to_ucsc( $file, $options, $append );
}
elsif ( $format eq "WIGGLE" )
{
$type = "wig 0";
- Maasha::UCSC::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
+ Maasha::UCSC::Wiggle::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
}
unlink $file;
Maasha::UCSC::ucsc_update_config( $options, $type );
-Maasha::Filesys::dir_remove( $tmp_dir );
+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();
}
__END__
-