[BioPython] Regarding GenBank

[Kael Fischer]

Sameet, et al:

In my experience, there definitely is an upper limit on the size of the 
genbank file you can index, and when you go over that limit you get exactly 
that error.

Furthermore, apropos of Brads reply, files that fail for this reason can be 
split and indexed fine - hence the minimal file that creates the problem is 
the enormous beast that crashed the parser, not any particular record or 
pair of records. (I have not gone back and checked this in 1.30)

I believe this has been discussed on the list before.  I recall that it was 
attributed to underlying text handling libraries, and not the GenBank 
module per se.

You might try a smaller file or iterating though the large one, if you can 
get away without random access to the records.

Regards,
Kael

At 11:32 PM 8/11/2004, Sameet Mehta wrote:
>Hi all,
>I am getting strange problems with the indexing of the GenBank file.  Is
>there any upper limit on the size of GenBank file that can be indexed.

[snip]

>Is there any bug?
>
>regards
>Sameet
>
>--
>National Centre for Cell Science, Pune
>
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--
Kael Fischer, Ph.D.
DeRisi Lab, University of California San Francisco