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| library("biomaRt") | |
| getPromoterSequence <- function(geneID, flankLeft, mart) { | |
| return(getBM( | |
| attributes = c("ensembl_gene_id",'coding_transcript_flank'), | |
| checkFilters=FALSE, filters = c('ensembl_gene_id','upstream_flank'), | |
| values=list(geneID, flankLeft), | |
| mart=mart, verbose=FALSE)) | |
| } | |
| getMart <- function(geneID, database='ENSEMBL_MART_PLANT') { | |
| ensemblDatabase <- useMart(database) | |
| ensemblDatasets <- listDatasets(ensemblDatabase) | |
| ensemblMart <- logical(0) | |
| geneChromosome <- logical(0) | |
| # Choosing dataset | |
| for (dataset in ensemblDatasets$dataset) { | |
| ensemblMart <- useDataset(dataset,mart=ensemblDatabase) | |
| geneChromosome <- getBM(attributes=c('chromosome_name'), | |
| filters='ensembl_gene_id', | |
| values=geneID, | |
| mart=ensemblMart) | |
| if ( | |
| # R version compatibility | |
| (class(geneChromosome) == 'data.frame' && dim(geneChromosome) [1] != 0) || | |
| (class(geneChromosome) == 'integer' && length(geneChromosome) != 0)) | |
| return(ensemblMart) | |
| } | |
| stop("GeneID not found") | |
| } | |
| getFasta <- function(sequence, gene) { | |
| fasta = paste(">", gene, sep="") | |
| fasta = paste(fasta, "| Length:", sequence$promoter_length, "| Genes: ", sequence$genes, | |
| "| Pseudogenes: ", sequence$pseudogenes, '|', sep=' ') | |
| fasta = paste(fasta,'\n', sep=' ') | |
| fasta = paste(fasta, sequence$coding_transcript_flank, '\n', sep='') | |
| return(fasta) | |
| } | |
| findPromoter <- function(geneID, ensemblMart) { | |
| geneStrand <- getBM(attributes=c('strand'), | |
| filter='ensembl_gene_id', | |
| values=geneID, | |
| mart=ensemblMart) | |
| geneChromosome <- getBM(attributes=c('chromosome_name'), | |
| filters='ensembl_gene_id', | |
| values=geneID, | |
| mart=ensemblMart) | |
| flankLeft <- 3000 | |
| # Forward strand | |
| if (geneStrand == 1) { | |
| transcriptStart <- getBM(attributes=c('transcript_start'), | |
| filter='ensembl_gene_id', | |
| values=geneID, | |
| mart=ensemblMart) | |
| if (class(transcriptStart) == "data.frame"){ | |
| transcriptStart <- min(transcriptStart[,1]) | |
| } else { | |
| transcriptStart <- min(transcriptStart) | |
| } | |
| promoterEnd <- transcriptStart - 1 | |
| promoterStart <- transcriptStart - (flankLeft + 1) | |
| } | |
| # Reverse strand | |
| if (geneStrand == -1) { | |
| transcriptStart <- getBM(attributes=c('transcript_end'), | |
| filter='ensembl_gene_id', | |
| values=geneID, | |
| mart=ensemblMart) | |
| if (class(transcriptStart) == "data.frame"){ | |
| transcriptStart <- max(transcriptStart[,1]) | |
| } else { | |
| transcriptStart <- max(transcriptStart) | |
| } | |
| promoterStart <- transcriptStart + 1 | |
| promoterEnd <- transcriptStart + (flankLeft + 1) | |
| } | |
| genesList <- as.data.frame( | |
| getBM(attributes = c('ensembl_gene_id', 'start_position', 'end_position', 'strand'), | |
| filters = c('chromosome_name','start','end', 'biotype'), | |
| values=list(geneChromosome, promoterStart, promoterEnd, 'protein_coding'), | |
| mart=ensemblMart)) | |
| pseudogenesList <- as.data.frame( | |
| getBM(attributes = c('ensembl_gene_id', 'start_position', 'end_position', 'strand'), | |
| filters = c('chromosome_name','start','end', 'biotype'), | |
| values=list(geneChromosome, promoterStart, promoterEnd, 'pseudogene'), | |
| mart=ensemblMart)) | |
| # Strip promoter ( + R version compatibility) | |
| if(class(genesList) == 'data.frame' && dim(genesList) [1] != 0) { | |
| if (geneStrand == 1) { | |
| promoterLength <- max(transcriptStart - 50 - max(max(genesList$end), 0),0) | |
| } | |
| else { | |
| promoterLength <- max(max(min(genesList$start), 0) - 50 - transcriptStart,0) | |
| } | |
| } else { | |
| promoterLength <- 3000 | |
| } | |
| # Chceck if promoter is empty | |
| if(promoterLength == 0) { | |
| sequence <- data.frame(coding_transcript_flank='') | |
| } else { | |
| sequence <- getPromoterSequence(geneID, promoterLength, ensemblMart) | |
| } | |
| sequence$promoter_length <- promoterLength | |
| sequence$genes <- toString(genesList$ensembl_gene_id) | |
| sequence$pseudogenes <- toString(pseudogenesList$ensembl_gene_id) | |
| return(sequence) | |
| } | |
| main <- function(inputFile, database='ENSEMBL_MART_PLANT') { | |
| genes <- read.table(inputFile, header=FALSE) | |
| for (gene in genes$V1) { | |
| tryCatch ( | |
| { | |
| mart <- getMart(geneID=gene, database=database) | |
| sequence <- findPromoter(geneID=gene, ensemblMart=mart) | |
| cat(getFasta(sequence, gene)) | |
| }, | |
| waring = function(w) {}, | |
| error = function(e) { write(paste(">", gene, " | ", e, sep=""), stderr()) } | |
| ) | |
| } | |
| } |
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Requirements:
R >= 2.15.1, <= 2.15.3
biomaRt == 2.14.0
Limitations
Supported version of ENSEMBL Plants Database: 16 (some genes may be unavailable)
Usage:
Sample input
Sample output: