[ensembl-dev] Getting variation consequence predictions without perl
Asraniel
asraniel at fryx.ch
Tue Sep 14 15:04:37 BST 2010
Thank you for your answer.
I do use the xml api of biomart. So i think there i'm on the save side.
I'm developing a bam alignment viewer in java that is deployed trough
webstart. This means the easiest way to go is in pure java.
I use ensembl to get live information, for example about the gene/transcripts
i'm currently looking at. The variations in the sequence file should then be
calculated on the fly for their consequences (even though some precalculation
might happen in the future).
So perl is really out of question. But at least now i know better what is
possible and what not, and what parts i have to develop myself.
Thank you
Beat Wolf
Am Dienstag 14 September 2010, um 15.54:30 schrieb Andreas Kahari:
> I'm just quietly wondering why you necessarily want to do this in
> Java... Are the tools (language) part of the problem specification
> you've been given? Wouldn't you be able to install the SNP effect
> predictor on one machine and then make it available to the Macs, Windows
> machines, and Linux boxen that needs access to it over HTTP? This is,
> after all, what we do on our live site.
>
> It seems to me that if the 3rd-party Java API (which I personally
> know nothing about) is complete enough to handle coordinate mappings
> (including HAP/PAR regions and SeqEdits etc.), and if it understands the
> variation schema and mimics the Perl API somewhat in what objects it
> can create from it, then that (i.e. porting the SNP effect predictor to
> Java) is your best alternative bet. The people developing the Java API
> would probably be very happy to see this happen, I imagine.
>
> Regarding mart: Remember that the Ensembl marts are *summaries* of what
> we have in the Core, Variation, FuncGen, Compara (etc.) databases,
> available for bulk query, and that the structure of the mart databases
> themselves might change without much warning. I would think carefully
> before writing an application on top of mart, especially if the
> application relies on the mart database schema instead of the existing
> XML-based API. The real data is in the other databases and we have
> (Perl) APIs for them that take into account changing schemas. Please
> use these primarily.
>
>
> Andreas
>
> On Tue, Sep 14, 2010 at 02:54:57PM +0200, Asraniel wrote:
> > 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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