[BioPython] Regarding GenBank

[Sameet Mehta]

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 -------