-#!/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::Plot;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
+my ( $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
$default = "plot_matches";
$terminals = "dumb,x11,aqua,post,svg";
close $fh;
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
foreach $match ( @{ $matches } )
{
- if ( $match->{ "DIR" } =~ /^f/ )
+ if ( ($match->{ "DIR" } and $match->{ "DIR" } =~ /^f/) or ($match->{ "STRAND" } and $match->{ "STRAND" } eq '+') )
{
print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";
close $fh_forward;
close $fh_backward;
- $cmd = "gnuplot";
+ $cmd = "gnuplot -persist";
$pid = open2( $fh_out, $fh_in, $cmd );
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__
-