[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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