Because <> can do two different things, readline and glob (and in your case is doing the wrong one), you should explicitly say while(readline($opts{-handle})).

So, if I changed the sub to have a local $fh it would do the right thing?

sub from_handle {
    my $self = shift;
    my %opts = @_;
    my $fh = $opts{-handle};
    while (<$fh>) {
        #... and here we're supposed to read from FH
    }
}
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Yes, that would work, but why not just use readline() directly?

What exactly do you have in the <> brackets? Can you post the code?

Also, now that you're using IO::File you can use its getline method instead of angle brackets to do linewise input. This eliminates the ambiguity with file globbing. See the docs for IO::File parent class, IO::Handle.

Okay, so here's the whole code. This sub is the one calling the parser:

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;
    }
}
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The call is 9 physical lines from the bottom. And here's the one who gets called:

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;
}
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And in the second block $_ == GLOB(0xa0bb570).

What happens if you replace the while line in from_handle with

while ( defined( $_ = $opts{-handle}->getline ) ) {
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?

the lowliest monk