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cebel / pyuniprot

Python package to query and analyse UniProt
Apache License 2.0
22 stars 8 forks source link

Memory problem with update #10

Closed cebel closed 7 years ago

cebel commented 7 years ago

Machines with low memory (<=8GB) have already problems with

import pyuniprot
pyuniprot.update(taxids=(9606,10090,10116))

Perhaps caching should be avoided and/or lxml (causes memory leak) have to be exchanged against python lib.

cebel commented 7 years ago

memory leak in XML parser, solved with clear() and SQLAlchemy (solved with sessionmaker -> expire_on_commit=True)