[ensembl-dev] Effects predictor version 2

[Graham Ritchie]

Hi Andrea,

We only have sift and polyphen predictions for variants which are predicted to result in single amino acid substitutions.

Cheers,

Graham

On 17 May 2011, at 15:37, Andrea Edwards wrote:

> Hello
> 
> Whilst looking into Stuart's question I looked at the variants on chromosome 1 out of curiosity and found that most of them don't have sift/polyphen data.
> Is this correct or have i made a mistake in my understanding of the schema
> 
> variants on chr1 (seq_region_id = 27511) 
> ============================ 
> 
> mysql> select count(*) from transcript_variation tv inner join 
> homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id = 
> tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript t on 
> t.transcript_id = st.transcript_id where t.seq_region_id = 27511; 
> +----------+ 
> | count(*) | 
> +----------+ 
> | 9633745 | 
> +----------+ 
> 1 row in set (3.34 sec) 
> 
> 
> variants on chr1 without sift and polyphen 
> =========================== 
> 
> mysql> select count(*) from transcript_variation tv inner join 
> homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id = 
> tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript t on 
> t.transcript_id = st.transcript_id where t.seq_region_id = 27511 and 
> tv.sift_prediction is null and tv.polyphen_prediction is null; 
> +----------+ 
> | count(*) | 
> +----------+ 
> | 9562313 | 
> +----------+ 
> 1 row in set (11.22 sec) 
> 
> 
> variants on chr1 with sift and polyphen 
> ========================= 
> 
> mysql> select count(*) from transcript_variation tv inner join 
> homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id = 
> tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript t on 
> t.transcript_id = st.transcript_id where t.seq_region_id = 27511 and 
> tv.sift_prediction is not null and tv.polyphen_prediction is not null; 
> +----------+ 
> | count(*) | 
> +----------+ 
> | 67919 | 
> +----------+ 
> 1 row in set (11.19 sec) 
> 
> 
> 
> thanks
> 
> 
> On 17/05/11 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 
>> 
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> 
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