[Bioperl-l] swissprot giving no id exception

[Ewan Birney]

On Mon, 15 Apr 2002, Guoneng Zhong wrote:

> Oh right, I looked at your code earlier and I see that it is -verbose 
> and I put in verbose.  I replaced the stream method with accessing each 
> id at a time.  That way worked with no problem, so it can't be the 
> accession numbers.  So it's working now, but it didn't work using the 
> following code:
> 
> 	while(@subarr = splice @ids,0,$MAX_IDS_SENT){
> 		print "Starting a another batch...\n";
> 		my $sp = new Bio::DB::SwissProt;
> 		my $sequenceIO = $sp->get_Stream_by_acc(\@ids);
> 		my $seqObj = 1;
> 		while($seqObj){
> 			eval{
> 				$seqObj = $sequenceIO->next_seq();
> 				if($seqObj){
> 					push @seqs,$seqObj;
> 					print $seqObj->primary_id."\n";
> 				}
> 			};
> 			print "uh oh:\n$@\n" if($@);
> 		}
> 	}
> 
> 
> Do you see anything wrong?  The exception is thrown only at the last 
> round of the outer while loop when the remaining ids were sent to 
> creating the stream.  There were 70 ids to start with, and 25 were sent 
> each time (apparently this DB object only allows something like 50 ids 
> sent at a time).

What was the exception? Same again?


Have you made use of perl -d to debug


in general people wont really have to time to debug your own code here, so
please make sure that you think the bug truely is in bioperl before you
just post here as soon as things go wrong. (or rather, feel free to post,
but don't expect other people to find your bugs... ;)).




> 
> G
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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