On 17 May 2006, at 15:54, David Withers wrote:
Arek Kasprzyk wrote:
On 17 May 2006, at 12:33, David Withers wrote:
Another question for you. When I send the following query to the
martservice I get an error message returned. Can anyone tell me what
I'm
doing wrong?
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" count="0">
<Dataset name="hsapiens_gene_ensembl">
<Filter name="gene_stable_id" value="ENSG00000100031" />
</Dataset>
<Dataset name="hsapiens_genomic_sequence">
<Attribute name="coding_gene_flank" />
</Dataset>
<Dataset name="hsapiens_gene_ensembl_structure">
<Attribute name="gene_stable_id" />
</Dataset>
<Links source="hsapiens_gene_ensembl"
target="hsapiens_gene_ensembl_structure"
defaultLink="hsapiens_internal_transcript_id" />
<Links source="hsapiens_gene_ensembl_structure"
target="hsapiens_genomic_sequence" defaultLink="coding_gene_flank" />
</Query>
Hi David,
the error was actually thrown on the server side but not propagated to
you - sorry.
It says
Wed May 17 13:44:10 2006] [error] -------------------- EXCEPTION
--------------------
DATE: 17-MAY-2006
MSG: Requests for flank sequence must be accompanied by an
upstream_flank or downstream_flank request
you just need to add this to your query:
<Filter name="upstream_flank" value="100" />
Hi Arek,
Is it possible to work out from the config xml that you need to add
this
filter (and that its value is 100)? Or does it need to be a hard coded
rule.
Yes, It is yet another pointer attribute. For example look at
agambiae_gene_ensembl dataset
xml under attribute group 'sequence', attribute collection 'upstream'
and the filter
is called: agambiae_genomic_sequece.filter.upstream_flank
The '100' value is user-defined. I could be anything from 1 to 9999.
Have a look
at
http://www.biomart.org/biomart/martview/NtLiZBboU5.mart
This value is provided in the 'Upstream flank' box
a.
The config for upstream_flank says that it's of type list, but doesn't
specify any options and I can't find anywhere where a value of 100 is
specified.
David.
--
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
Tel: +44(0)161 275 0145
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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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