[Biopython-dev] UniProt GOA parser

[Iddo Friedberg]

A new uniprot-GOA parser is available for you to poke around:

https://github.com/idoerg/biopython/tree/uniprot-goa/Bio/UniProtGOA

More on Uniprot-GOA: http://www.ebi.ac.uk/GOA

There are three file formats: GAF (gene association file) , GPA (gene
product association) and GPI (gene product information) explained here:
http://www.ebi.ac.uk/GOA/downloads

Input GAF files can be very large, due to the growth of uniprot GOA. If you
would like to test in a timely fashion, I suggest you get historical files,
which are smaller. Once you get to the > 40 version numbers, the runtime
for the example code in UniProtGOA.py goes over 2 minutes (on my i5
machine).

Old GAF files are available here:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/old/UNIPROT/

Current GPI and GPA files are not very large.

Thanks to Peter for his help on this.

Best,

Iddo
-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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