[ensembl-dev] Effects predictor version 2

[Graham Ritchie]

Hi Stuart,

The script just reads precomputed sift and polyphen predictions from the database. Do you have copies of the sift_prediction and polyphen_prediction tables in your local database (along with the supporting protein_info and protein_position tables)?

Cheers,

Graham


On 17 May 2011, at 13:59, Stuart Meacham wrote:

> Hello,
> 
> Thanks for the reply.
> 
> On 17/05/11 13:35, Will McLaren wrote:
> 
>> 
>> This is strange - are you sure you are checking out the branch and not
>> the head of the API? You should be doing something like:
>> 
>> cvs checkout -r branch-ensembl-62 ensembl
>> cvs checkout -r branch-ensembl-62 ensembl-variation
> 
> Actually I just used the links from the site here:
> 
> http://www.ensembl.org/info/docs/api/api_installation.html
> 
> the link(s) resolve to things like:
> 
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-62&view=tar
> 
>> 
>>> 
>>> The script silently over-writes an existing output file of the same name,
>>> this seems a bit brutal, perhaps the default should be to fail if the file
>>> exists.
>> 
>> I think this is pretty standard behaviour for command-line programs. I
>> could change it to only run if in an output file name is specified
>> perhaps?
> 
> Yes, probably it's standard behaviour. I was just imagining accidentally overwriting a file the script had spent 24 hours creating . . .
> 
>> 
>> That's also odd - any variants classified as non-synonymous coding
>> should have a "SIFT=*" entry in the final column. Can you try the
>> attached file as input on your system?
>> 
> 
> No problem, the command I used was:
> 
> perl ./variant_effect_predictor_2.pl -r reg.pl -i ./test.txt -w -b 100000 --sift=p --polyphen=p --failed=0 -terms=so
> 
> and the output (no errors but also no predictions) is attached.
> 
> Cheers
> 
> Stuart
> <variant_effect_output.txt>_______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/