-#!/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::Filesys;
$num = 1;
- while ( $record = Maasha::UCSC::PSL::psl_get_entry( $data_in ) )
+ while ( $entry = Maasha::UCSC::PSL::psl_entry_get( $data_in ) )
{
- Maasha::Biopieces::put_record( $record, $out );
+ if ( $record = Maasha::UCSC::PSL::psl2biopiece( $entry ) )
+ {
+ Maasha::Biopieces::put_record( $record, $out );
- last if $options->{ "num" } and $num == $options->{ "num" };
+ last if $options->{ "num" } and $num == $options->{ "num" };
- $num++;
+ $num++;
+ }
}
close $data_in;
}
+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();
}