-#!/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::Filesys;
use Maasha::NCBI;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
+my ( $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
$fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip, $file );
$options = Maasha::Biopieces::parse_options(
$soft_index = Maasha::NCBI::soft_index_file( $file );
+ # print STDERR Dumper( $soft_index ) if $options->{ "verbose" };
+
$fh = Maasha::Filesys::file_read_open( $file );
@platforms = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
close $data_in if $data_in;
close $fh if $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();
}