[go] map2slim problems

[Seth Carbon]

On Thu, 2008-02-07 at 16:14 +0100, Erika Feltrin wrote:
> Dear all,
> 
> I am using map2slim perl script to group proteins annotate by GOA into
> the GO categories listed in the Plant GO slim. I have tried map2slim
> with small file as test, and it worked.
> Unfortunately, when I run it using the proper files nothing happend.
> I am usign a 2G RAM machine.

I have tried running this, but without a lot of success:

perl -I /users/sjcarbon/local/src/cvs/go-dev/go-perl
-I /users/sjcarbon/local/src/cvs/go-dev/go-db-perl map2slim
-c /users/sjcarbon/tmp/gene_ontology_edit.obo /tmp/goa_uni

The gene association file unzips to about four and a half gigabytes, and
in short order used up all of my memory and swap, and then exited
without a whisper. This would suggest a memory problem, but I'm not sure
of a way around it.

Cheers,

-Seth


> The input file that I am using for this script are:
> 
> PlantGOslim .obo file
> http://www.geneontology.org/GO_slims/goslim_plant.obo
> 
> Gene Ontology .obo file 
> http://www.geneontology.org/ontology/gene_ontology_edit.obo
> 
> GOA annotations file
> ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
> 
> Does anybody have any idea on what is the problem?
> 
> Thanks
> Erika
> 
> 
> 
> 
>