[ensembl-dev] Getting variation consequence predictions without perl

Asraniel asraniel at fryx.ch
Tue Sep 14 13:54:57 BST 2010


Thank you.

i guess i have to understand the way transcripts are stored in biomart, and 
the calculate the consequence by myself. For basic stuff it looks easy enough.
I just have digg a little more into genetics. After what i have read a 
transcript can have one "5' UTR ", but it seems like every exon can have one.

What CDS End/Start is i can guess, but why a Genomic coding end/start is also 
there, no idea yet. What exactly a cDNA coding are is is also a mystery 
currently, i thought that the CDS was coding... 

Is there a place where the structure of the transcripts in the DB is 
documented? I tried wikipedia to understand it. Hope i'll get there.

Beat Wolf

Am Dienstag 14 September 2010, um 14.34:47 schrieb Pontus Larsson:
>   Ok, those consequences have to be calculated on-the-fly by the API and
> are not stored in the database. Hence, BioMart will not be useful to you
> in this respect. Unless you can wrap the perl code like Stuart
> suggested, I believe your best bet would be the kind of third-party API
> that Andrew mentioned.
> 
> Cheers
> /Pontus
> 
> On 14/09/2010 13:14, Asraniel wrote:
> > 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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