Hi Bob, there are some pointers on this page: http://www.biomart.org/martservice.html
a On Thu, Jan 12, 2012 at 8:50 AM, Bob Freeman <[email protected]>wrote: > 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.pmline >> 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* > > > > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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