[Bioperl-l] Bio::DB::Fasta

Staffa, Nick (NIH/NIEHS) staffa at niehs.nih.gov
Wed Jun 6 10:40:49 EDT 2007


Indeed.
One must know what is actually in his header,
AND 
one must write the appropriate make_id subroutine
AND
one must specify the exact ID.
THEN things might work.
And they did!
THANK YOU


On 6/6/07 2:06 AM, "Torsten Seemann"
<torsten.seemann at infotech.monash.edu.au> wrote:

> Nick,
> 
>> Can't call method "seq" on an undefined value at Match-emNEWTEST.pl line 84,
> 
> The error makes it pretty clear. You are calling the ->seq method on
> an undefined value, ie. $pse_obj.
> 
>> my $pse_obj = $db->get_Seq_by_id('GA17307');
> 
> # check we got something!
> die "sequence not in database" unless $pse_obj;
> 
>> my $pse_sequence = $pse_obj->seq;
> 



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