-#!/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::Align;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $entry );
+my ( $options, $in, $out, $record, @entries, $entry );
$options = Maasha::Biopieces::parse_options();
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) { # TODO use biopieces2fasta() instead
push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
} elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
}
}
+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__
-