[BioC] MySQL mode is not available in biomaRt?

[Vincent Carey]

   From the man page for v 2.1.0 of biomaRt, running under R 2.10:

  local: MySQL access to Ensembl is no longer supported.  biomaRt in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

   mysql: MySQL access to Ensembl is no longer supported.  biomaRt in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

    user: MySQL access to Ensembl is no longer supported.  biomaRt in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

password: MySQL access to Ensembl is no longer supported.  biomaRt in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

my suggestion is to remove the mysql parameter setting from your call
and proceed as you used to.  if you get errors on subsequent queries
write a new email to the list.  be sure to read carefully the man page
for the functions you are using before using them.  also, you can get
sequence data without web service if you have BSgenome.Mmusculus...
package installed.  Check the annotation/metadata package pages.


On Sun, Nov 14, 2010 at 12:44 PM, Takashi Kodama <takashi at salk.edu> wrote:
> Dear all,
>
> I used to use MySQL mode of biomaRt to retrieve genomic sequence using simple chromosome coordinate (e.g. chr 1, 100000-100100). I did work fine. However, recently I update biomaRt to 2.6.0, and found that MySQL mode was no longer implemented, at least in the same way. Could anybody tell me how to use MySQL mode with biomaRt 2.6.0, or if there is alternative way to get genomic sequence using simple chromosome coordinate?
>
> Below is  the error message I got;
>
>> library("biomaRt")
>> ensembl = useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl", mysql=TRUE)
> Error in useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl",  :
>  unused argument(s) (mysql = TRUE)
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.6.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3 XML_3.2-0
>
> Thank you!
> Takashi
> ------------------------------------------------------------
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Rd., La Jolla, CA 92037
> Phone: +1-858-453-4100 x1788
> FAX: +1-858-455-7933
> Email: takashi at salk.edu
>
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