Thanks, Junjun. Don't mean to be so dense, but how do I use this?? I'm a Biomart casual user (though an expert programmer), so I need just a little hand-holding.
-b On Jan 11, 2012, at 10:37 PM, Junjun Zhang wrote: > Hi Bob, > > If you download protein sequences for the entire human genome. As this will > be a long running query, it would help if this can be split into multiple > queries, say one query for each chromosome. Shown as below is to retrieve > protein sequences on chromosome 1. > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName = "default" formatter = "FASTA" header = "0" > uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > > > <Dataset name = "hsapiens_gene_ensembl" interface = "default" > > <Filter name = "chromosome_name" value = "1"/> > <Attribute name = "peptide" /> > <Attribute name = "ensembl_gene_id" /> > <Attribute name = "ensembl_transcript_id" /> > </Dataset> > </Query> > Hope this helps! > > Junjun > > > > From: Arek Kasprzyk <[email protected]> > Date: Wed, 11 Jan 2012 10:55:50 -0500 > To: Bob Freeman <[email protected]> > Cc: "[email protected]" <[email protected]>, jzhang > <[email protected]>, Jonathan Guberman <[email protected]> > Subject: Re: Timeouts on queries > >> Hi Bob, >> I am forwarding your email to the users mailing list to let the server >> administrators know that there is a problem with sequence retrieval. >> >> >> a >> >> >> On Wed, Jan 11, 2012 at 10:42 AM, Bob Freeman <[email protected]> >> wrote: >>> Hit this problem last week, and it appears it is still happening this >>> morning (US east coast time). >>> >>> Your results file FAILED. >>> >>> Here is the reason why: >>> >>> DBD::mysql::st execute failed: Lost connection to MySQL server during query >>> at >>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm >>> line 209. >>> >>> >>> Please try your request again, or alternatively contact your service >>> provider >>> including a copy of this email and quoting this reference: >>> martquery_0111103024_649.txt.gz. >>> >>> Am trying to download human proteins with 6 additional attributes in the >>> header. >>> >>> Hope you can bring this to the attention of the relevant persons. >>> >>> Cheers! >>> Bob >>> >>> ----------------------------------------------------- >>> Bob Freeman, Ph.D. >>> Acorn Worm Informatics, Kirschner lab >>> Dept of Systems Biology, Alpert 524 >>> Harvard Medical School >>> 200 Longwood Avenue >>> Boston, MA 02115 >>> 617/432.2294, vox >>> >>> "Sorry I'm late. Oh, God, that sounded insincere. I'm late." >>> -- Karen Walker, from Will and Grace >>> >>> >>> >>> >>> >> >> >> >> -- >> Arek Kasprzyk, MD, MSc, PhD >> BioMart Project Lead >> ----------------------------------------------------- Bob Freeman, Ph.D. Acorn Worm Informatics, Kirschner lab Dept of Systems Biology, Alpert 524 Harvard Medical School 200 Longwood Avenue Boston, MA 02115 617/432.2294, vox "Sorry I'm late. Oh, God, that sounded insincere. I'm late." -- Karen Walker, from Will and Grace
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