[ensembl-dev] Getting variation consequence predictions without perl

Stuart Meacham sm766 at cam.ac.uk
Tue Sep 14 11:39:54 BST 2010

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 

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is obviously out of date.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!



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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