[Bioperl-l] Bio::DB::GenPept server error

[Neil Saunders]

Dear all,

Still having problems with Bio::DB::GenPept, get_Stream_by_id().

I have a test file, containing 3 UIDs separated by commas.  If I read in
this file and assign it to an array:

open IN,'test.file';
@array=<IN>;

then my code works fine and retrieves what I want using \@array.

Now I move to my real file, which contains about 112 000 UIDs.  Same
procedure and I get:

MSG: WebDBSeqI Request Error:
500 (Internal Server Error) short write

Is this because the server doesn't like such a large file, or some other
problem?  Should I even be using this module to retrieve 112 000
records?  I would get them using fastacmd from a local nr database, but
the required -i option seems to be broken (gives duplicate records).

thanks for any pointers,
Neil
-- 
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php