[Bioperl-l] Bioperl-db doesn't seem to load all entries

pelikan at cs.pitt.edu pelikan at cs.pitt.edu
Mon Dec 4 17:34:59 EST 2006


    My system is running bioperl 1.5.2, bioperl-db 1.5.2-005 RC, and the
latest mySQL under Windows, Activeperl, without Cygwin. I have 4 GB
memory. "make test"s past fine.

The problem is that I'm not getting similar numbers of anything when I
load datasets using load_seqdatabase.pl. For instance, if I want to load
only protiens from Homo Sapiens,
I go to UniProt,
use the database search function,
do a text search for Homo Sapiens (returns 70914 hits),
export the hits to flat file format (--format swiss) using the data set
and load it using load_seqdatabase.pl.

The result of  "select count(*) from bioentry;" results in only 1003 entries.
Moreover it seems like the entries don't go past the B's in the alphabet -
I can't find bioentry.descriptions like '%cytochrome%' or '%myoglobin%',
but I can find apolipoproteins, for example.

I know this is an annoying question, but if someone has more experience in
dealing with this issue, I would be grateful for any assistance. I don't
get any error messages, so it's difficult for me to tell what's going on.


More information about the Bioperl-l mailing list