[Bioperl-l] error while remote blast against swissprot db

Chris Fields cjfields at uiuc.edu
Mon Apr 16 19:24:32 EDT 2007


What version of bioperl are you using?  I get an error but it is b/c  
the ID doesn't exist.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: acc KPYK_ECOLI does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/cjfields/src/bioperl-live/Bio/ 
Root/Root.pm:359
STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /Users/cjfields/src/bioperl- 
live/Bio/DB/WebDBSeqI.pm:181
STACK: genpept.pl:21
-----------------------------------------------------------

The actual accession is 'KPYK1_ECOLI'.

chris

On Apr 16, 2007, at 3:42 PM, DeeGee wrote:

>
> hi
> i tried the following code just to check the network, and it worked  
> fine
> except for the SwissProt part, for which i got the error message  
> instead of
> the sequence:
>
> ------------- EXCEPTION  -------------
> MSG: swissprot stream with no ID. Not swissprot in my book
> STACK Bio::SeqIO::swiss::next_seq
> /usr/perl5/5.6.1/lib/Bio/SeqIO/swiss.pm:179
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/perl5/5.6.1/lib/Bio/DB/WebDBSeqI.pm:187
> STACK toplevel bbbbb.pl:21
> --------------------------------------
>
> #### check #####
> #!/usr/bin/perl -w
> use strict;
> use Bio::DB::GenBank;
> use Bio::DB::SwissProt;
> use Bio::DB::GenPept;
> use Bio::SeqIO;
>
> my $genpeptdb = new Bio::DB::GenPept();
> my $genbankdb = new Bio::DB::GenBank();
> my $swissdb = new Bio::DB::SwissProt();
>
> my $seqio = new Bio::SeqIO(-format => 'fasta',
>                            -fh     => \*STDOUT);
>
> my $protseq = $genpeptdb->get_Seq_by_acc('O26717');
> $seqio->write_seq($protseq);
>
> my $seq = $genbankdb->get_Seq_by_acc('AF303112');
> $seqio->write_seq($seq);
>
> $protseq = $swissdb->get_Seq_by_acc('KPY1_ECOLI');
> $seqio->write_seq($protseq);
>
> thanks a lot.
>
>
> Chris Fields wrote:
>>
>> The 'verbose' setting doesn't change the way the BLAST query is sent,
>> it just sends the raw output from the repeated attempts to retrieve
>> the report (using the RID) to STDERR.  The error you saw won't be
>> fixed by doing so.
>>
>> What I was interested in was the raw HTML output dumped to the
>> screen.  If it is querying the NCBI server it should dump stuff that
>> includes something like this:
>>
>> ...
>> <HTML>
>> <p></p>
>> <!--
>> QBlastInfoBegin
>>          Status=WAITING
>> QBlastInfoEnd
>> --><p></p>
>> <SCRIPT LANGUAGE="JavaScript"><!--
>> ...
>>
>> which indicates you have a request in the BLAST queue.  If you aren't
>> seeing anything then the problem is likely network-related on your
>> end, so getting the latest RemoteBlast won't help.  Do any other
>> BioPerl modules requiring network access work (Bio::DB::GenBank, for
>> instance)?  If not it could be a proxy issue...
>>
>> Just in case, here's the browsable CVS location for RemoteBlast:
>>
>> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/
>> Tools/Run/RemoteBlast.pm?cvsroot=bioperl
>>
>> Click on the download link and save over your local version.
>>
>> chris
>>
>> On Apr 16, 2007, at 2:10 PM, DeeGee wrote:
>>
>>>
>>> hi Chris,
>>> thanks for your reply. i set the RemoteBlast factory to a verbosity
>>> of 1,
>>> and i get the same error message. i'm new to all these. so, could
>>> you plz
>>> tell me how can i do the RemoteBlast in CVS that you've suggested.
>>>
>>> cheers!!!
>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
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> remote-blast-against-swissprot-db-tf3577674.html#a10024333
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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