[BioC] Retrieving Upstream Sequences With biomaRt

[Peter Robinson]

Hi Conductors,

I have been experimenting with the very nice biomaRt package and noticed in the vignette (section 5) that sequence retrieval appears to be restricted to the cDNA (possibly only UTR) or peptide sequences. From an earlier posting on the mailing list, I saw a way to retrieve upstream sequences:

library(biomaRt)
ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl", mysql=TRUE)
entrez <- c("100","330")
gene <- getGene(id=entrez, type="entrezgene", mart=ens)
getSequence(chromosome = gene$chromosome, start = gene$start - 2000, end= gene$end + 1000, mart=ens)


However, when I try the following line:


gene <- getGene(id=entrez, type="entrezgene", mart=ens)

I get the error message

Error in mysqlExecStatement(conn, statement, ...) :
        RS-DBI driver: (could not run statement: Can't create/write to file '/ensembldb1b-1/data/#sql_21c2_0.MYI' (Errcode: 13))


The examples in the vignette all seem to work. What is wrong here? Where is the file mentioned in the error message supposed to live? 

Thanks, Peter