[BioPython] GenBank Parser and large files?

Stephan Herschel Stephan.Herschel at biovertis.com
Tue Mar 15 12:23:10 EST 2005


   Hi,
   I'm parsing some genebank files. When parsing large files it appears
   the parser eats up all of my memory until nothing is left, i.e. it's
   not possible to parse large files (>25 MB).
   That's the way I do it:
   >>> from Bio import GenBank
   >>> fh=open(fname,'r')
   >>> feature_parser=GenBank.FeatureParser()
   >>> gb_iterator = GenBank.Iterator(fh, feature_parser)
   >>> cur_record = gb_iterator.next()
   Is there a way to circumvent this problem?
   Thanks,
   Stephan



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