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
> ------------------------------------------------------------------------
> -------
>
>
