[BioC] biomaRt getSequence through genomic position

[Wolfgang Huber]

Dear Paul,

and what is the output of sessionInfo()?

  bw Wolfgang

Paul Hammer ha scritto:
> hi all,
> 
> i try to get sequences via the getSequence function from biomaRt. Exact 
> i would like to have the last 5 bases of an exon and the last 5 bases of 
> the following intron. my approach is following:
> 
> library(biomaRt)
> ensembl_rat = useMart("ensembl", dataset="rnorvegicus_gene_ensembl")
> filter_rat = listFilters(ensembl_rat)
> rat_exonsLocs = getBM(attributes=c("ensembl_exon_id", 
> "exon_chrom_start", "exon_chrom_end"), filter=filter_rat[c(14,45,12),1], 
> values=list(chromosome="1", status="KNOWN", biotype="protein_coding"), 
> mart=ensembl_rat)
> laenge = dim(rat_exonsLocs)[1]
> 
> ensembl_rat2 = useMart("ensembl", dataset="rnorvegicus_gene_ensembl", 
> mysql=TRUE)
> for(i in 1:laenge){
> gseqs_exon = getSequence(chromosome = 1, start=rat_exonsLocs[i,3]-5, end 
> = rat_exonsLocs[i,3], mart = ensembl_rat2)
> seqs_introns = getSequence(chromosome = 1, start=rat_exonsLocs[i+1,2]-5, 
> end=rat_exonsLocs[i+1,2], mart = ensembl_rat2)
> }
> 
> but i get always this error message: "Error in mysqlNewConnection(drv, 
> ...) : RS-DBI driver: (??O?cannot allocate a new connection -- maximum 
> of 16 connections already opened)"
> 
> Is there a way to use useMart without mysql=TRUE to get sequences only 
> via genomic position? when i connect without mysql=TRUE 
> (useMart("ensembl", dataset="rnorvegicus_gene_ensembl") ) i always have 
> to set seqType and type. when i do this i don't get the 5 bases that i 
> want!
> 
> any help would great!
> thanks in advance
> paul
>