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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1747





------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2005-03-10 04:52 -------
While "working" with the GenBank parser and this patch, I think I got a rough
idea of how Martel is intended to work - and very clever it is too.  Its a pity
it does not scale well.

I agree with Andrews point that any Martel parser is much harder to get to grips
with than a format specific hand writen parser (e.g. the BLAST parser).

P.S. Timings and memory needs with the first patch (#198 - still using Martel
for the "header section") and the second patch (#200 - no Martel dependance) are
more or less the same.

If anyone interested in testing this, and could produce some memory footprint
information automatically, that would be welcome.



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