39 lines
1.4 KiB
R
39 lines
1.4 KiB
R
#' @title Import data file
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#' @description Imports data from several formats (FASTA, VCF, SAM, BAM).
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#' @param data raw dataset
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#' @param format data format (guesses from extension if not provided)
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#' @param verbose if \code{TRUE}, prints extra output information
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#' @return The data in a format that can be used by the other functions
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#' @export
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#' @examples
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#' path_inst <- system.file("extdata", "", package = "rBAPS")
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#' importFile(file.path(path_inst, "FASTA_clustering_haploid.fasta"))
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importFile <- function(data, format, verbose) {
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# Parsing data format ------------------------------------------------------
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if (missing(format)) {
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format <- gsub(".*\\.(.+)$", "\\1", data)
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message("Format not provided. Guessing from file extension: ", format)
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}
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format <- tolower(format)
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# Dispatching to proper loading function -----------------------------------
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if (format == "fasta") {
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out <- load_fasta(data)
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} else if (format == "vcf") {
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out <- vcfR::read.vcfR(data, verbose = verbose)
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} else if (format == "sam") {
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stop(
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"SAM files not directly supported. ",
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"Install the samtools software and execute\n\n",
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"samtools view -b ", data, " > out_file.bam\n\nto convert to BAM ",
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"and try running this function again with 'format=BAM'"
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)
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} else if (format == "bam") {
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out <- Rsamtools::scanBam(data)
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} else {
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stop("Format not supported.")
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}
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return(out)
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}
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