[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
Tue Nov 8 05:13:41 EST 2005


------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-08 05:13 -------
OK, revised instructions:-

(1) Apply my patch to Bio/GenBank/__init__.py

(2) Remove the old file Bio/ReseekFile.py in favour of just

(3) Update FormatIO.py line 4:

Change 'import ReseekFile'
To 'from Bio.EUtils import ReseekFile'

(4) Update Bio/config/DBRegistry.py line 229:

Change 'from Bio.ReseekFile import ReseekFile'
To 'from Bio.EUtils.ReseekFile import ReseekFile'

Then Michael's example in comment 7 using GenBank.NCBIDictionary works.

(My grep skills are a bit rusty, but I didn't notice any other uses of

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