#' @import data.table
#' @import testit
read_exstra_db_known <- function(file, ...) {
if (!is.character(file)) stop("file must be character")
data <- read.delim(file, stringsAsFactors = FALSE, comment.char = "#", ...)
testit::assert("Known requires Disease or locus column", ! is.null(data$Disease) || ! is.null(data$locus))
if(is.null(data$Disease)) {
testit::assert("Known requires Disease or locus column", ! is.null(data$locus))
data$Disease <- data$locus
}
data <- replace(data, data == "NA", NA)
data$locus <- sub(".*\\((.*)\\).*", "\\1", data$Disease, perl = T)
# Match the first suitable column
names(data)[checkmate::assert_int(grep("chr(om)?$", names(data), TRUE))] <- "chrom"
names(data)[checkmate::assert_int(grep("start(\\.0)?$", names(data), TRUE))] <- "chromStart"
names(data)[checkmate::assert_int(grep("end$", names(data), TRUE))] <- "chromEnd"
# give more verbose repeat number information
exstra_db_new_(data, "named")
}
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