[Biopython-dev] [Bug 1747] GenBank parser is very slow and memory hungry for large input files

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 7 18:47:26 EST 2005


------- Comment #10 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-07 18:47 -------
Mystery solved: There are two different ReseekFile.py files in BioPython.  The
one I changed (based on tracing the exception thrown) lives in

Revision: 1.3, Sun Mar 21 16:56:53 2004 UTC (19 months, 2 weeks ago) by

There is second version in Bio/EUtils/ReseekFile.py which appears to be more
advanced (more comments, supports readline, readlines, ...)

Revision: 1.1, Fri Jun 13 00:49:37 2003 UTC (2 years, 4 months ago) by dalke 

This version is however "older", but this is only due to a minor comment
related change by Brad Chapman on the first file.

It looks like Bio/ReseekFile.py should be removed, and Bio/EUtils/ReseekFile.py
used instead.  Andrew Dalke's implementation of readline is a safer bet than my
quick hack, plus he included some test cases for it as well. 

I haven't tried this yet as it late here, and I need to go to sleep now instead

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