[ensembl-dev] Getting variation consequence predictions without perl

[Pontus Larsson]

  Ok, those consequences have to be calculated on-the-fly by the API and 
are not stored in the database. Hence, BioMart will not be useful to you 
in this respect. Unless you can wrap the perl code like Stuart 
suggested, I believe your best bet would be the kind of third-party API 
that Andrew mentioned.

Cheers
/Pontus


On 14/09/2010 13:14, Asraniel wrote:
> I got that part.
> But this only tells me the variants that are already known.
>
> I want to know the consequence of a random variant at a random position not
> yet know.
> The perl api can tell me what the consequence is for a specific transcript.
> Biomart does not seem to allow me to do that...
>
> Beat Wolf
>
> Am Dienstag 14 September 2010, um 13.58:55 schrieben Sie:
>>    Yes, Ensembl Variation ->  Homo Sapiens Variation will get you human
>> variation data. To get the transcript consequences, you'll find them
>> under Attributes ->  Gene associated information ->  Consequence to
>> transcript.
>>
>> There is also the option to filter results by consequence, you'll find
>> that under Filters ->  Gene associated variation filters ->  Consequence
>> type.
>>
>> Hope this helps!
>> /Pontus
>>
>> On 14/09/2010 12:04, Asraniel wrote:
>>> Sounds great.
>>>
>>> I'm no biologist, so i'm not sure what biomart to choose.
>>>
>>> For the known variations i use:
>>> Ensembl Variation 59
>>> Homo sapiens Variation (dbSNP 131; ENSEMBL).
>>>
>>> what would i have to choose for the predicted variants?
>>>
>>> thank you
>>>
>>> Beat Wolf
>>>
>>> Am Dienstag 14 September 2010, um 12.58:39 schrieben Sie:
>>>>     Hi,
>>>>
>>>> There is a dedicated BioMart for Ensembl Variation data which contains
>>>> the predicted transcript consequences
>>>> (http://www.ensembl.org/biomart/martview). Could you extract them from
>>>> there?
>>>>
>>>> Cheers
>>>> /Pontus
>>>>
>>>> On 14/09/2010 11:42, Asraniel wrote:
>>>>> Thanks for your answer.
>>>>>
>>>>> Sadly this is not an option, because my app has to work on
>>>>> linux/windows/mac and is started trough webstart, so i can't expect
>>>>> that everybody has a perl interpreter installed.
>>>>>
>>>>> Beat Wolf
>>>>>
>>>>> Am Dienstag 14 September 2010, um 12.39:54 schrieb Stuart Meacham:
>>>>>> Hi there,
>>>>>>
>>>>>> This is probably not going to answer your question! However I also
>>>>>> developed a Java app and wanted to use the SNP consequence prediction
>>>>>> script (or variations thereof). My first attempt was to just execute
>>>>>> the script from within the app with a call to:
>>>>>>
>>>>>> ///////////////
>>>>>>
>>>>>> Process p = Runtime.getRuntime().exec("/path/to/script/script.pl");
>>>>>>
>>>>>> //////////////
>>>>>>
>>>>>> and then reading the output of the script with:
>>>>>>
>>>>>> //////////////
>>>>>>
>>>>>> BufferedReader stdInput = new BufferedReader(new
>>>>>> InputStreamReader(p.getInputStream()));
>>>>>>
>>>>>> String s = null;
>>>>>>
>>>>>> while ((s = stdInput.readLine()) != null) {
>>>>>>
>>>>>> 	//do stuff with s
>>>>>>
>>>>>> }
>>>>>>
>>>>>> //////////////
>>>>>>
>>>>>> This works fine although can be slow, and the speed is erratic,
>>>>>> especially if your app is going to support many concurrent users. In
>>>>>> order to traverse this problem I implemented a second version which
>>>>>> simply ran the script independently (outside the app) saved the output
>>>>>> to a database and read the database from the app.
>>>>>>
>>>>>> I do remember having a conversation once with an Ensembl Dev who said
>>>>>> that there was a Java API a few years ago but it now lacks support and
>>>>>> is obviously out of date.
>>>>>>
>>>>>> Good luck!
>>>>>>
>>>>>> Stuart
>>>>>>
>>>>>> On 14/09/10 11:22, Asraniel wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> i'm developing java app and i access the ensembl data trough biomart.
>>>>>>> Works great, thanks for that api.
>>>>>>>
>>>>>>> Now, is there a way to get the variantion consequence prediction
>>>>>>> without using perl? i didn't find a way trough biomart.
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Beat Wolf
>>>>>>>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pontus Larsson, Ph.D.
Ensembl Variation

EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
UK
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~