apologies, please note the typo corrections,
On Sat, 2007-11-17 at 19:27 +0000, Syed Haider wrote:
> Hi David,
> for both perl and webservice APIs, it will look like a normal filter
> representing a genomic region (chr,start,end). If you see on Biomart
> MartView, Ensembl Gene -> human, under filters you can see 'Encode
> region' which has preset values. You should be able to assign your own
> set of values for the new genomic region filter just the same. You would
> be able to upload as many segments as you want to.
>
> for instance, in webservice call,
>
> <Filter name = "genomic_region" value = "7:115597757:117475182"/>
>
> or
>
> <Filter name = "genomic_region" value =
> "7:115597757:117475182,1:100:100000,12:1000000,4000000"/>
^^^^
:
>
> equivalent perl API call would be
> $query->addFilter("genomic_region", ["7:115597757:117475182"]);
> or
> $query->addFilter("genomic_region",
> ["7:115597757:117475182,1:100:100000,12:1000000,4000000"]);
^^^^
:
>
> Hope that will enable you to feed biomart system with multiple region
> value.
>
> regards
> syed
>
>
> On Sat, 2007-11-17 at 19:10 +0000, Arek Kasprzyk wrote:
> > On 14 Nov 2007, at 07:32, David M. Goodstein wrote:
> >
> > > I was wondering if there are any shortcuts that enable UCSC table
> > > browser-style intersection queries in BioMart. The typical
> > > application would be to grab all the genes that overlap a given set of
> > > sequences (e.g., ESTs) aligned to the reference genome. Or does one
> > > need to retrieve all the spans for the alignments in questions and
> > > then directly query BioMart for overlap with each span?
> > >
> >
> > Hi David,
> > Syed (cc'ed on this email) looked into the fix in more detail and it
> > appears that we would be able to implement it with not too much
> > trouble.
> > This means that we could add it to the existing ensembl mart config to
> > be available for your even as early as ensembl 48 (scheduled for early
> > december)
> > would it work for you?
> >
> > Syed, could you give David a code snippet for the api and web service
> > of how this would work in theory so we could make sure that this is
> > what he wants before implementing anything? :)
> >
> > cheers,
> > a.
> >
> >
> >
> > > regards,
> > > -David
> > >
> > >
> > > David M. Goodstein
> > > Computational Genomics Group
> > > Joint Genome Institute
> > > Lawrence Berkeley National Lab
> > >
> >
> >
> > ------------------------------------------------------------------------
> > -------
> > Arek Kasprzyk
> > EMBL-European Bioinformatics Institute.
> > Wellcome Trust Genome Campus, Hinxton,
> > Cambridge CB10 1SD, UK.
> > Tel: +44-(0)1223-494606
> > Fax: +44-(0)1223-494468
> > ------------------------------------------------------------------------
> > -------
> >
> >
