For starters, I don't understand both Bio:DB::Das::Chado and Bio::DB::Das::Chado::Segment being subclasses of Bio::Root::Root ... but besides that I also don't think this line is doing what you want:

return $self->Bio::DB::Das::Chado::Segment->new($name,$self,$start,$end);

shouldn't that just be: 

return Bio::DB::Das::Chado::Segment->new($name,$self,$start,$end);

[download]

Other than that, are you sure your sql is returning results? If your sql fails, $cvterm_id will never be converted to a hash reference (it will stay a plain scalar) and your code downstream will fail. You probably want something like this to protect the code downstream (or you could check if you have a hash downline): 

my $cvterm_id = {} ;  # this scalar is  a hashref
while (my $hashref = $sth->fetchrow_hashref) {
    $$cvterm_id{$$hashref{termname}} = $$hashref{cvterm_id};
}

[download]

Then at least %termhash will be a hash but quite possibly an empty one if the sql fails.

-derby

In reply to Re: Hash references moving between modules by derby
in thread Hash references moving between modules by scain

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