[Biopython-dev] [Bug 2738] Speed up GenBank parsing, in particular location parsing

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 29 18:26:09 UTC 2009


------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-29 13:26 EST -------
Created an attachment (id=1209)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1209&action=view)
Simple test script for checking GenBank location parsing

This is a simple script to help validate the location parsing has not changed. 
Intended usage is to put the script in a directory with a good set of test
GenBank files (all ending with the extension .gbk), then:

(starting with a clean install of Biopython)

$ time python parse_gbk_locs.py > old.txt

(apply the patch)

$ time python parse_gbk_locs.py > new.txt

(verify the output matches)

$ ls -l old.txt new.txt

(check file sizes agree)

$ diff old.txt new.txt

(should be no output)

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