Created
May 23, 2011 01:40
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Convert TopHat GTF to Bioconductor TranscriptDB
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GTF2TranscriptDB <- function(gtf.file, out.file = NULL, verbose = TRUE) | |
{ | |
require(rtracklayer) | |
require(GenomicRanges) | |
require(GenomicFeatures) | |
min.info <- c("gene_id", "transcript_id", "exon_number") | |
if (verbose) message("Importing ", gtf.file) | |
gtf <- import.gff(gtf.file, asRangedData = FALSE) | |
#parse the per exon attributes | |
if (verbose) message("Parsing gene/transcript/exon ids.") | |
exon.info <- strsplit(gsub("\"|;", "", values(gtf)$group), split=" ") | |
exon.info <- lapply(exon.info, function(x) { | |
data <- x[seq(2, length(x), 2)] | |
names(data) <- x[seq(1, length(x), 2)] | |
data | |
}) | |
attribs <- names(exon.info[[1]]) | |
if (!all(min.info %in% attribs)) stop("Not all required attributes are in this GTF file.") | |
exon.info <- do.call(data.frame, c(lapply(attribs, function(x) | |
sapply(exon.info, "[", x)), | |
stringsAsFactors = FALSE)) | |
colnames(exon.info) <- attribs | |
values(gtf) <- exon.info | |
if (verbose) message("Creating tables.") | |
#make transcripts table | |
exons.by.tx <- split(gtf, values(gtf)$transcript_id) | |
transcripts <- data.frame( | |
tx_id = 1:length(exons.by.tx), | |
tx_name = names(exons.by.tx), | |
tx_chrom = as.character(seqnames(unlist(exons.by.tx))[start(exons.by.tx@partitioning)]), | |
tx_strand = as.character(strand(unlist(exons.by.tx))[start(exons.by.tx@partitioning)]), | |
tx_start = IRanges::sapply(start(ranges(exons.by.tx)), min), | |
tx_end = IRanges::sapply(end(ranges(exons.by.tx)), max), | |
stringsAsFactors = FALSE) | |
#make exons table | |
exons.ord <- unlist(exons.by.tx) | |
splicings <- data.frame( | |
tx_id = rep(1:length(exons.by.tx), elementLengths(exons.by.tx)), | |
exon_rank = as.integer(values(exons.ord)$exon_number), | |
exon_chrom = as.character(seqnames(exons.ord)), | |
exon_strand = as.character(strand(exons.ord)), | |
exon_start = start(exons.ord), | |
exon_end = end(exons.ord), | |
stringsAsFactors = FALSE) | |
#make genes table | |
gene.txs <- tapply(values(gtf)$transcript_id, values(gtf)$gene_id, unique) | |
genes <- data.frame( | |
tx_name = unlist(gene.txs), | |
gene_id = rep(names(gene.txs), sapply(gene.txs, length)), | |
stringsAsFactors = FALSE) | |
#create the db | |
if (verbose) message("Creating TranscriptDb.") | |
gtf.db <- makeTranscriptDb(transcripts, splicings, genes) | |
if(!is.null(out.file)) | |
{ | |
if (verbose) message("Writing database to file.") | |
saveFeatures(gtf.db, out.file) | |
} | |
gtf.db | |
} |
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