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
>
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