# ================================================================
# functions for reading gff files
# https://stat.ethz.ch/pipermail/bioconductor/2008-October/024669.html
# ================================================================
getAttributeField <- function (x, field, attrsep = ";") {
s = strsplit(x, split = attrsep, fixed = TRUE)
sapply(s, function(atts) {
a = strsplit(atts, split = "=", fixed = TRUE)
m = match(field, sapply(a, "[", 1))
if (!is.na(m)) {
rv = a[[m]][2]
}
else {
rv = as.character(NA)
}
return(rv)
})
}
gffRead <- function(gffFile, nrows = -1, skip = 0) {
cat("Reading ", gffFile, ": ", sep="")
gff = read.table(gffFile, sep="\t", as.is=TRUE, quote="",
header=FALSE, comment.char="#", nrows = nrows, skip = skip,
colClasses=c("character", "character", "character", "integer",
"integer",
"character", "character", "character", "character"))
colnames(gff) = c("seqname", "source", "feature", "start", "end",
"score", "strand", "frame", "attributes")
cat("found", nrow(gff), "rows with classes:",
paste(sapply(gff, class), collapse=", "), "\n")
stopifnot(!any(is.na(gff$start)), !any(is.na(gff$end)))
return(gff)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.