[Bioperl-l] RE: more on Genscan.pm

[Osborne, Brian]

Hilmar,

>> (BTW feel free to add this yourself to the Genscan tests if you feel up
to it.)

Why don't I give it a try, what could I possibly do wrong?          ;-)

Thanks again,

Brian O.



 -----Original Message-----
From: 	Hilmar Lapp [mailto:hlapp@gmx.net] 
Sent:	Friday, November 30, 2001 11:18 AM
To:	Osborne, Brian
Cc:	Bioperl
Subject:	Re: more on Genscan.pm

"Osborne, Brian" wrote:
> 
> Hilmar,
> 
> One thing that's nice about this module is that I can ask if something's
> defined, and avoid fatalities :
> 
> $genscan = Bio::Tools::Genscan->new( -file => "test" );
> while ( $gene = $genscan->next_prediction ({
>         my $pep = $gene->predicted_protein;
>         print $pep->display_id if ( defined $pep );
> }
> But, I can't seem to be able to test for "defined $genscan". This test is
> useful when confronted with a file like the one I'm attaching.
> <<test.genscan>>
> 

(Note: the file was a prediction with only one promoter, and hence
no sequence predicted at all. The parser crashed on this one, as
well as complaining about a number of undefined values when using
-w.)

Brian, this was obviously a bug. I fixed it on main trunk as well
as 0.7.x branch. I still have to add the according test for it.
(BTW feel free to add this yourself to the Genscan tests if you
feel up to it.)

	-hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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