[ensembl-dev] Effects predictor version 2

Stuart Meacham sm766 at cam.ac.uk
Tue May 17 13:59:13 BST 2011


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:


the link(s) resolve to things like:


>> 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.


-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: variant_effect_output.txt
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110517/23bdb201/attachment.txt>

More information about the Dev mailing list