[Biopython-dev] UniProt GOA parser

[Peter Cock]

Thanks Aravind,

It looks the same to me at first glance, and seems to work:

from Bio.UniProt import GOA
with open("go_Gene_association.txt") as handle:
    for record in GOA.gafiterator(handle):
        print record

Iddo - can you see anything to worry about in your code?
Can we add a note to this module that it can be used on
other non-UniProt GO Annotation files?

Thanks,

Peter

On Wed, Jun 4, 2014 at 3:36 PM, Venkatesan <Aravind.Venkatesan at lirmm.fr> wrote:
> Hello Peter,
>
> This link to the Gramene gaf downloads
> ftp://ftp.gramene.org/pub/gramene/archives/PAST_RELEASES/release31/data/ontology/go/
>
> I have also attached a sample file that I made for parsing purpose.
>
> thanks,
>
> Aravind
>
> On 04/06/2014 16:26, Peter Cock wrote:
>>
>> Hi Aravind,
>>
>> The Gramene downloads page http://www.gramene.org/ftp-download
>> talks about all sorts of formats but not GAF.
>>
>> Could you give us a specific example (e.g. the URL) of one of the
>> files you are hoping to parse?
>>
>> Thanks,
>>
>> Peter
>>
>> On Wed, Jun 4, 2014 at 3:09 PM, Venkatesan <Aravind.Venkatesan at lirmm.fr>
>> wrote:
>>>
>>> Hello all,
>>> I am new to Biopython. I need to parse a couple of GAF files provided by
>>> Gramene database (http://gramene.org/),  they contain associations for
>>> genes
>>> and qtl  to gene ontology but also to plant ontology, trait ontology (gaf
>>> 1.0 format). Is the parser uniport specific or is it a generic parser for
>>> GAF files. Your inputs are very much appreciated.
>>>
>>> Thank you,
>>
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>
>
> --
> Aravind Venkatesan
> Post-doctoral Researcher,
> Computational Biology Institute,
> Laboratory of Informatics, Robotics and Microelectronics of Montpellier
> (LIRMM),
> France
>
>
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