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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: