[ensembl-dev] Getting variation consequence predictions without perl

[Pontus Larsson]

  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
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list
>>>>> Dev at ensembl.org
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
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>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pontus Larsson, Ph.D.
Ensembl Variation

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