On 9 May 2006, at 18:13, Amir Karger wrote:
I modified the simple example script from biomart-plib. It's attached.
(The registry file is just a copy of the default one.)
Hi Amir,
can you copy your script in the body of this email and post it again so
we can look into this
in more detail? (This lists only accepts text and no attachments).
When I try to run it, I get the results below. If I delete
hsapiens_gene_ensembl_structure.exon_stable_id from @names, it works
just fine and gives me ID & description for the two genes (although
there's two copies of BRCA2. Hm). Why am I getting a web server error
by
adding an extra attribute?
In order to avoid you rhaving to answer more questions... is there a
good biomart-plib tutorial or documentation to read?
The only documentation that we have at the moment is on
http://www.biomart.org/install.html (pdf). I don't think this contains
a lot of info but you should find something there. We'll try to write
a better section about API for 0.5
Obviously I can
look at the POD, but that's too detailed. And I can look at the sample
files, but there are only a few - and they don't explain general
concepts anyway.
Thanks,
- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
Harvard University
617-496-0626
ps Arek, thanks for your quick response to my connection question.
------------------------------
perl try.pl
Software/configuration version check: 0.4 DICTYBASE (NORTHWESTERN) OK
Software/configuration version check: 0.4 ENSEMBL 38 (SANGER) OK
Software/configuration version check: 0.4 SEQUENCE 38 (SANGER) OK
Software/configuration version check: 0.4 SNP 38 (SANGER) OK
Software/configuration version check: 0.4 VEGA 38 (SANGER) OK
Software/configuration version check: 0.4 UNIPROT 4-5 (EBI) OK
Software/configuration version check: 0.4 MSD 4 (EBI) OK
Software/configuration version check: 0.4 WORMBASE CURRENT (CSHL) OK
DATASET default ... ENSEMBL 38 (SANGER) ...... ..........
hsapiens_gene_ensembl ..................... (WEB) www.biomart.org:80
............ OK
hsapiens_gene_ensembl_structure.gene_stable_id at try.pl line 44.
hsapiens_gene_ensembl_structure.exon_stable_id at try.pl line 44.
description at try.pl line 44.
Problems with the web server: 500 Internal Server Error
No Rows Returned
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Subject: newbie: how to find allowed attributes
Date: Tue, 9 May 2006 13:13:03 -0400
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Thread-Topic: newbie: how to find allowed attributes
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From: "Amir Karger--
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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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