[Bioperl-l] swissprot giving no id exception

[Guoneng Zhong]

Yup, my version was like 0.7.  So I downloaded the tar ball from bioperl 
site and installed it.

However, the problem persists (with the exception thrown).  I tried 
adding a verbose flag as you recommended, and this is what I got:

-------------------- WARNING ---------------------
MSG: Requested Format verbose is ignored because only SwissProt and 
Fasta formats are currently supported
---------------------------------------------------
------------- EXCEPTION  -------------
MSG: Must specify a known host, not 1, possible values (uk)
STACK Bio::DB::SwissProt::hostlocation 
/Library/Perl/Bio/DB/SwissProt.pm:375
STACK Bio::DB::SwissProt::new /Library/Perl/Bio/DB/SwissProt.pm:166
STACK HypotheticalProteinSearch::retrieveSequences 
HypotheticalProteinSearch.pm:35
STACK main::retrieveList retrieve_gpi.pl:56
STACK toplevel retrieve_gpi.pl:15

--------------------------------------


I will now try using just one accession number at a time.  Strange how 
the stream didn't work...

G

On Saturday, April 13, 2002, at 12:11 AM, Jason Stajich wrote:

> We make sure the VERSION is Bio::Seq module reflects the version number
> of the package.
>
> % perl -MBio::Seq -e 'print "Version is ", $Bio::Seq::VERSION, "\n";'
>
> As to your problem - stream mode should be working - we have a test for
> this in the DB.t test so it may be something specific about the 
> accession
> numbers - I would first try and retrieve the seqs by doing
>
> my @seqs;
> foreach my $acc ( @accs ) {
>   my $seq = $db->get_Seq_by_acc($acc);
>   push @seqs, $seq;
> }
>
> FYI - you can try and debug code yourself by turning on the debug flag
>
> my $sp = new Bio::DB::SwissProt(-verbose => 1);
>
> See Bio::Root::Root /Bio::Root::RootI for more information about how the
> verbose flag works (setting it to 1 will print out the debug statements
> in the SwissProt module).
>
>
> -j
> On Fri, 12 Apr 2002, Guoneng Zhong wrote:
>
>> 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
>>>> -------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l@bioperl.org
>>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> --
>>> Jason Stajich
>>> Duke University
>>> jason@cgt.mc.duke.edu
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>
>
>