[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 21:13:19 UTC 2009


------- Comment #7 from bsouthey at gmail.com  2009-01-29 16:13 EST -------
(In reply to comment #4)
> > While the number of records and sequences are the same, I have not checked if
> > the patched version is providing exactly the same output as the unpatched
> > version. This is very important for the different types of GenBank files
> > (Whole Genome Shotgun and CON types).
> I agree through testing is important here.  Would you like to suggest any
> particular WGS or CON files for testing with? 

I downloaded a few example files including WGS and CON. I found that CON files
are not parsed by either version. Not a surprise given that these have no
sequences but that is a different topic. Apart from the errors in attached
case, I have not seen any other errors (even parsing the references).


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