[Biopython-dev] Parsing Protein GenBank Records

[Brad Chapman]

[Talking about the GenBank parser]
Jeong:
> The updated parser now works well for most REFSEQ
> proteins. I came across several REFSEQ protein records where the parser
> still fails on UNIX machine. The following is the error message:
>
> I just found out that this problem occurs on some REFSEQ nucleotide records
> as well.

Thanks for the heads up. I've done a lot of work on the GenBank parser
and run it across a lot of human chromosome 1 from RefSeq, and it now
seems to be acting right for me. There were a bunch of fixes to file in
Bio/GenBank (genbank_format.py, __init__.py, LocationParser.py and
Record.py) and to Bio/SeqFeature.py to handle RefSeq decently.

I've committed all of the changes to CVS, so if you have the most recent
CVS everything should work smoothly with RefSeq (I hope :-). I hope this
will also fix the problems that Peter was reporting.

If you still have problems, please don't hesitate to let me know and
I'll work more on it. Let me know what files you're having problems
with, and I can take a look at those specificially.

Enjoy!
Brad