[BioPython] Genbank parsing problem and fix

[Peter]

gca500 at york.ac.uk wrote:
> Hi All,
> 
> Been having a problem using the Genbank RecordParser with some Genbank 
> files that have recently been added to NCBI. After a bit of trial and 
> error, I realised the problem only occurs if a REFERENCE field isn't 
> followed by an AUTHOR field (for example in reference 2 of this record: 
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=88602864).
> 
> There's a very easy fix on line 289 of Genbank.py. Decided to post this to 
> the list to save any one else who stumbles across this problem tearing 
> their hair out like I've been doing this afternoon!
> 
> Change ... and it works!
> 
> Hope this is useful,
> 
> Gemma

Hi Gemma,

I have made your suggested change to biopython/Bio/formatdefs/genbank.py 
as CVS revision 1.10, which should be viewable online soon:

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

I am curious as to why you are using this code (part of the FormatIO 
system), rather than the Bio.GenBank module.

Thank you,

Peter