sub parse {
    my $self = shift;
    my @opts = @_;
    my %opts;
    if ( ! @opts || scalar @opts % 2 ) {
        $self->COMPLAIN("bad number of arguments.");
        return;
    }
    else {
        %opts = @opts;
        if ( ! $opts{-format} || ! grep(ucfirst($opts{-format}), @pars
+ers) ) {
            $self->COMPLAIN("no valid format specified.");
            return;
        }
        if ( $opts{-file} && ( ! -T $opts{-file} || ! -r $opts{-file} 
+) ) {
            $self->COMPLAIN("file not found, not a text file, or not r
+eadable");
            return;
        }
        elsif ( ! $opts{-file} && ! $opts{-string} ) {
            $self->COMPLAIN("no data source specified.");
            return;
        }
        my $lib = ref $self;
        $lib .= '::' . ucfirst($opts{-format});
        eval "require $lib";
        my $parser = new $lib;
        if ( $opts{-file} && $parser->can('from_handle') ) {
            open(FH, $opts{-file});
            $opts{-handle} = \*FH;
            return $parser->from_handle(%opts);
        }
        if ( $opts{-string} && $parser->can('from_string') ) {
            return $parser->from_string(%opts);
        }
        $self->COMPLAIN("the parser can't handle the data source speci
+fied");
        return;
    }
}
[download]

sub from_handle {
    my $self = shift;
    my %opts = @_;
    my $taxa = new Phylo::Taxa;
    my $version = $self->VERSION;
    while (<$opts{-handle}>) {
        if ( $_ ) {
            my $taxon = new Phylo::Taxa::Taxon;
            my $date = localtime;
            my $description = qq{Read from $opts{-file} using Phylo ve
+rsion $version on $date};
            $taxon->name($_);
            $taxon->desc($description);
            $taxa->insert($taxon);
        }
    }
    return $taxa;
}
[download]

What happens if you replace the while line in from_handle with

while ( defined( $_ = $opts{-handle}->getline ) ) {
[download]

?

the lowliest monk