[Biopython-dev] UniProt GOA parser

[Venkatesan]

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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!DB     DB_Object_ID    DB_Object_Symbol        Qualifier       GOid    DB:Reference    Evidence        With(or)From    Aspect  DB_Object_Name  DB_Object_Synonym       DB_Object_Type  Taxon   Date    Assigned_by
GR_gene GR:0060141      CL              GO:0007275      GR_REF:1793     IMP             P       CLUSTERED SPIKELETS     Cl|Clustered spikelets  Gene    taxon:4530      20100422
        GR
GR_gene GR:0060146      [CMS-BO]                GO:0005739      GR_REF:6006     IMP             C       CYTOPLASMIC MALE STERILITY BO   [cms-bo]|`Chinsurah boro 2' cytoplasm|[cms-bo]|'Chinsurah boro II' cytoplasm    Gene    taxon:4530      20100422        GR
GR_gene GR:0060146      [CMS-BO]                GO:0007275      GR_REF:6006     IMP             P       CYTOPLASMIC MALE STERILITY BO   [cms-bo]|`Chinsurah boro 2' cytoplasm|[cms-bo]|'Chinsurah boro II' cytoplasm    Gene    taxon:4530      20100422        GR
GR_gene GR:0060153      [CMS-IR66707A]          GO:0007275      GR_REF:5552     IMP             P       CYTOPLASMIC MALE STERILITY IR66707A     Oryza perennis Acc. 104823 cytoplasm|[cms-IR66707A]|Oryza perennis Acc104823 cytoplasm  Gene    taxon:4530      20100422        GR
GR_gene GR:0060154      [CMS-KALINGA-I]         GO:0007275      GR_REF:5870     IMP             P       CYTOPLASMIC MALE STERILITY KALINGA      [cms-Kalinga-I]|[cms-Kalinga-I]|Cytoplasmic controlled cold tolerance   Gene    taxon:4530      20100422        GR
GR_gene GR:0060154      [CMS-KALINGA-I]         GO:0009409      GR_REF:5870     IMP             P       CYTOPLASMIC MALE STERILITY KALINGA      [cms-Kalinga-I]|[cms-Kalinga-I]|Cytoplasmic controlled cold tolerance   Gene    taxon:4530      20100422        GR
GR_gene GR:0080063      SaM             GO:0009556      GR_REF:25509    IMP             P       SaM     SaM+|SaM-       Gene    taxon:4530      20100422        GR
GR_gene GR:0080063      SaM             GO:0019789      GR_REF:25509    IMP             F       SaM     SaM+|SaM-       Gene    taxon:4530      20100422        GR
GR_gene GR:0080064      SaF             GO:0009556      GR_REF:25509    IMP             P       SaF     SaF+|SaF-       Gene    taxon:4530      20100422        GR
GR_gene GR:0080064      SaF             GO:0016829      GR_REF:25509    IMP             F       SaF     SaF+|SaF-       Gene    taxon:4530      20100422        GR
GR_gene GR:0090001      SOC1            GO:0003702      GR_REF:0        IMP             F       SUPPRESSOR OF OVEREXPRESSION OF CO 1    OsSOC1  Gene    taxon:4530      20100422
        GR