Hi Philippe, you need to look at the individual datasets not marts. There is an assembly version included in the dataset name.
Please let me know if you need more info a On Wed, Sep 14, 2011 at 10:25 PM, pip pipster <[email protected]> wrote: > Arek, > Thanks for the reply. Even on the ENSEMBL mart, it says 63 (but no > indication of patch level). For coordinates I suspect it's not all that > important, but for sequences it would be. If there's no other way then one > would have to manually determine the patch level by looking for a nucleotide > that's 'new' in a given patch. That's the approach I'll take if there's no > other way. But to do that everytime you pull data from a mart seems > overkill. > > Regards, > Phillipe > > ------------------------------ > *From:* Arek Kasprzyk <[email protected]> > *To:* pip pipster <[email protected]> > *Cc:* "[email protected]" <[email protected]> > *Sent:* Wednesday, September 14, 2011 5:51 PM > *Subject:* Re: [BioMart Users] Patch version determination > > Hi Philippe, > there is no explicit support for assembly version. The individual > administrators can of course use > place holders such a mart name or dataset name or description to put the > names there as you can see in ensembl or icgc examples > > a > > On Wed, Sep 14, 2011 at 3:28 PM, pip pipster <[email protected]> wrote: > > Does anyone know how to determine what patch level a given mart is using? > For example, if I use the following Mart, is it using GRCh37, GRCh37 Patch > 3, GRCh37 Patch 5, etc. ? I'm hoping there is a command you can issue in > Bioperl where the Mart tells you exactly which Assembly it's using but open > to any other avenue that would work. > > <MartURLLocation database="ensembl_mart_63" default="1" > displayName="ENSEMBL GENES 63 (SANGER UK)" host="www.biomart.org" > includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" > port="80" serverVirtualSchema="default" visible="1" /> > > Thank you, > Phillipe > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > > > >
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