I modified the simple example script from biomart-plib. It's attached. (The registry file is just a copy of the default one.)
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? 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
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---ATTENTION: MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This Mailing List at ebi.ac.uk only accepts PLAIN TEXT * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ------_=_NextPart_001_01C6738B.D4E518C6" X-MimeOLE: Produced By Microsoft Exchange V6.5 Subject: newbie: how to find allowed attributes Date: Tue, 9 May 2006 13:13:03 -0400 Message-ID: <[EMAIL PROTECTED]> X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Thread-Topic: newbie: how to find allowed attributes Thread-Index: AcZzi9TF/GzEIw2dTsS4Y5Ib9tvn8w== From: "Amir Karger--
