[ensembl-dev] Getting variation consequence predictions without perl

[Pontus Larsson]

  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 is obviously out of date.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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>> _______________________________________________
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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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~