[Bioperl-l] Bio::DB::GenBank batch mode usage

John Tyree johntyree at gmail.com
Wed Jul 1 19:36:33 UTC 2009

I'm trying to use Bio::DB::GenBank to download a large number of files
by accession number. The docs say not to do this in normal mode to
reduce server load. There is some kind of helper function associated
with this.

    %params = Bio::DB::GenBank->get_params('batch');

But I don't understand how to use it. If you pass the hash using:


it raises the following and dies:

--------------------- WARNING ---------------------
MSG: invalid retrieval type tool must be one of (pipeline,io_string,tempfile

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: seq_start() must be integer value if set
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::DB::NCBIHelper::seq_start
STACK: Bio::DB::NCBIHelper::new
STACK: Find_Patient_By_AccNo.pl:93

There is a deprecated method called get_Stream_by_batch() but how does
one achieve batch mode using the proper get_Stream_by_id() ?


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