[ensembl-dev] Effects predictor version 2
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
> 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
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.
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