[Bioperl-l] error from GenBank

Stefan Weckx stefan.weckx at vib.be
Wed Dec 29 11:31:54 EST 2004

hi all,

does anybody have experience with this:

I'm retrieving data from GenBank (protein/nucleotide) using 
Bio::DB::Query::GenBank within a loop, based on a list of taxonomy ids 
referring to bacterial strains. In case there is no data in GenBank for 
a certain strain, I get an error message (see below) and the script 
terminates ... which is not the behaviour I would like to see, since 
there are still other taxid's waiting for being queried ...

more specifically, the Bio::DB::Query::GenBank query itself runs ok, 
only while extracting data with e.g. "my $count = $query->count" the 
error message appears and the script terminates.

Suggestions to work around this are welcome!


error message:

Warning(s) from GenBank:
------------- EXCEPTION  -------------
MSG: Error from Genbank: No items found.
STACK Bio::DB::Query::GenBank::_parse_response 
STACK Bio::DB::Query::WebQuery::_run_query 
STACK Bio::DB::Query::WebQuery::_fetch_ids 
STACK Bio::DB::Query::WebQuery::ids 
STACK toplevel ./harvest_LAB_ORF.pl:37

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