[ensembl-dev] Getting variation consequence predictions without perl

[Asraniel]

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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> >>>>> Dev at ensembl.org
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> >>>> 
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