view getmlst.pl @ 2:0f31ef2dfdde draft default tip

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#!usr/bin/env perl

use strict;
use warnings;
use Cwd;
use File::Copy;

my ($binary, $mlst_db, $mlst_defs, $species) = @ARGV;

$species =~ s/__pd__/#/ig;

my $command = "python $binary --species '$species'"; #add proper spaces to command

my $rv = system($command);

if ($rv == 0)
{
	#need to find output files in the dir
	my $cur_dir = getcwd();

	foreach my $file (<$cur_dir/*>)
	{
		if ($file =~ /\.fasta$/)
		{
			move($file, $mlst_db);
		}
		elsif ($file =~/\.txt$/)
		{
			move($file, $mlst_defs);
		}
	}
}
$rv = $rv >> 8;
exit $rv;