Perfect. Thank you. -b
On Jan 12, 2012, at 4:27 PM, Arek Kasprzyk wrote: > 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.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 >>> >>> >>> -- >>> Arek Kasprzyk, MD, MSc, PhD >>> BioMart Project Lead >>> > > > > > -- > 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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