[ensembl-dev] Getting variation consequence predictions without perl

[Asraniel]

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 is obviously out of date.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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