I think that would work quite well, as long as the regions could also
specify strand. Is that possible?
--David
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
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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
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