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lib/Bio/Tools/Run/EMBOSSacd.pm  view on Meta::CPAN

    my $version = `embossversion -auto`;
    my $file;
    if ($version lt "2.8.0") {
	# reading from EMBOSS program acdc stdout (prior to version 2.8.0)
	$file = `acdc $prog -help -verbose -acdtable 2>&1`;
    } else {
	# reading from EMBOSS program acdtable stdout (version 2.8.0 or greater)
	$file = `acdtable $prog -help -verbose 2>&1`;
    }

    # converting HTML -> XHTML for XML parsing
    $file =~ s/border/border="1"/;
    $file =~ s/=(\d+)/="$1"/g;
    $file =~ s/<br>/<br><\/br>/g;
    $file =~ s/&nbsp;//g;

    my $t = XML::Twig->new( TwigHandlers =>
			   {
			       '/table/tr' => \&_row  }
			   );