[Bioperl-l] error while remote blast against swissprot db
gdorjee at hotmail.com
Mon Apr 16 16:42:37 EDT 2007
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
------------- EXCEPTION -------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK toplevel bbbbb.pl:21
#### check #####
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');
my $seq = $genbankdb->get_Seq_by_acc('AF303112');
$protseq = $swissdb->get_Seq_by_acc('KPY1_ECOLI');
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:
> 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:
> Click on the download link and save over your local version.
> 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.
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> Bioperl-l at lists.open-bio.org
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