[BioPython] Regarding GenBank
Sameet Mehta
sameet at nccs.res.in
Thu Aug 12 23:32:00 EDT 2004
Hi,
The file that i was trying to index here has only 3 records!! And the file
per se is not a huge file. Irrespective of the number of records it gives
the same error!
Is there a way around this!
regards
Sameet
--
National Centre for Cell Science, Pune
---------- Original Message -----------
From: Kael Fischer <kael at sonic.net>
To: "Sameet Mehta" <sameet at nccs.res.in>, biopython at biopython.org
Sent: Thu, 12 Aug 2004 15:55:25 -0700
Subject: Re: [BioPython] Regarding GenBank
> 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
> >
> >_______________________________________________
> >BioPython mailing list - BioPython at biopython.org
> >http://biopython.org/mailman/listinfo/biopython
>
> --
> Kael Fischer, Ph.D.
> DeRisi Lab, University of California San Francisco
------- End of Original Message -------
More information about the BioPython
mailing list