[Bioperl-l] swissprot giving no id exception

[Guoneng Zhong]

I thought I have BioPerl 1.0.  How do I find out?  I thought I installed 
Bundle::BioPerl from CPAN, does that not work?  Actually, all it said, 
after installing the necessary modules, was that the modules all check 
out ok....

Is there a version or some trick I can use to find out which version is 
on the system?

G

On Friday, April 12, 2002, at 09:26  PM, Jason Stajich wrote:

> Which version of bioperl?
>
> On Fri, 12 Apr 2002, Guoneng Zhong wrote:
>
>> Hi,
>> I am wondering if others have this problem.  Here's my code, followed 
>> by
>> the exception thrown.  I get the same exception when I try to do a
>> next_seq on the sequenceIO object.  The array of ids I send is verified
>> to contain non-empty ids.  Now, I can't guarantee tht those ids are
>> valid, but if they are not, must an exception be thrown to ruin the
>> whole process?  I tried to "catch" the exception using "eval" but
>> stranger things happen, like next_seq would give me the same sequence
>> again!
>>
>> Thanks in advance!
>> G
>>
>> 		my $sp = new Bio::DB::SwissProt;
>> 		my $sequenceIO = $sp->get_Stream_by_acc(\@ids);
>> 		my $fh = $sequenceIO->fh;
>> 		my $tmp = <$fh>;
>>
>>
>> -------------------- EXCEPTION --------------------
>> MSG: swissprot stream with no ID. Not swissprot in my book
>> STACK Bio::SeqIO::swiss::next_seq /Library/Perl/Bio/SeqIO/swiss.pm:155
>> STACK Bio::SeqIO::READLINE /Library/Perl/Bio/SeqIO.pm:570
>> STACK HypotheticalProteinSearch::retrieveSequences
>> HypotheticalProteinSearch.pm:37
>> STACK main::retrieveList retrieve_gpi.pl:54
>> STACK toplevel retrieve_gpi.pl:14
>> -------------------------------------------
>>
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>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>