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@salk.edu [[alternative HTML version deleted]]

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 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >