Entering edit mode
Paul Hammer
▴
220
@paul-hammer-2635
Last seen 9.6 years ago
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
