[BioPython] Bug in Bio.GenBank.index_file()

[Jan T. Kim]

Hi all,

first off, I'm sorry for the delay in replying, it's been a very busy
week... (lame excuse, I know ;-)

Secondly, thanks a lot to Andrew & Brad for your replies. I've found
the discussion about locators etc. quite interesting. Having investigated
that bug, I had some notion that determining file coordinates for parser
events is not as easy as it might seem at first glance, but only after
seeing the discussion, I learned that concepts for solving this problem
are already available.

On Wed, May 16, 2001 at 05:18:19PM -0400, Brad Chapman wrote:

> Okay, understood. I'll be very happy to help with this, if I can. 
> GenBank indexing is very important to me, since I use it all of the
> time to serve out Sequence databases through Biocorba. I'm happy to do 
> this either through mindy (or something similar) or using the modified 
> Locator object idea you suggest in your other reply.
> 
> So, Jan, does using the working Mindy-based implementation that I've
> got now seem okay for your needs, until we have the opportunity to
> code up something more permanent?

Currently, we don't seriously need the GenBank dictionary access -- my
student tried to use it as he came across it in the tutorial (where it
is even advertised as a "very cool thing"), but when those problems
arose, I advised him to walk through his records with a GenBank.Iterator,
which works fine. I reported the bug because I found it and I thought
so I could just as well post that info before we're seriously bitten
ourselves...

Greetinx & thanx again, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
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