[BioPython] GenBank parsing

[Peter (BioPython)]

Kyle Dent wrote:
> Dear All,
> 
> My script was successfully implementing the Genbank
> parser until just today I was trying to get it to
> parse a genpept file. After much experimentation I
> discovered that it was actually having trouble parsing
> even newly downloaded GenBank files as well
> (downloaded of NCBI).
> 
> I wanted to ask if anyone is aware of this problem, I
> understand the flat file format was updated this month
> and is probably the cause of this.

I'm aware that earlier in 2006, there was a new project line added.  I 
haven't been aware of any further changes... on the other hand, I don't 
think I've ever used a "genpept" file either.

Anyway, from the error message you are using the "old" Martel based 
parser shipped with BioPython 1.41

We recommend you update to the current CVS parser which is (a) more up 
to date, (b) faster, (c) should give slightly more helpful error 
messages if it does get stuck.

For most cases you can simply download this file, replacing your 
Bio/GenBank/__init__.py after making a backup of the old version:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/GenBank/__init__.py?cvsroot=biopython

If you see errors about ReseekFile then you will need to make a few 
other changes...

If you are still having trouble, or need further help making the update, 
please reply back.  Including the GenBank reference of any problem file 
would be handy.

Thank you

Peter