biomaRt getSequence through genomic position
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Paul Hammer ▴ 220
@paul-hammer-2635
Last seen 10.3 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
biomaRt biomaRt • 1.0k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
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 >
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