[ensembl-dev] Getting variation consequence predictions without perl

Asraniel asraniel at fryx.ch
Tue Sep 14 12:04:04 BST 2010


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 is obviously out of date.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
> >> 
> >> _______________________________________________
> >> Dev mailing list
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> > 
> > _______________________________________________
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