50 lines
1.8 KiB
R
50 lines
1.8 KiB
R
#' @title Clustering of individuals
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#' @param data data file
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#' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"
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#' @param verbose if \code{TRUE}, prints extra output information
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#' @importFrom utils read.delim
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#' @importFrom vcfR read.vcfR
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#' @importFrom Rsamtools scanBam
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#' @importFrom adegenet read.genepop .readExt
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#' @references Samtools: a suite of programs for interacting
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#' with high-throughput sequencing data. <http://www.htslib.org/>
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#' @export
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greedyMix <- function(data, format, verbose = TRUE) {
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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 if (format == "genepop") {
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if (toupper(adegenet::.readExt(data)) == "TXT") {
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message("Creating a copy of the file with the .gen extension")
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dataGen <- gsub("txt", "gen", data)
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file.copy(data, dataGen)
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out <- adegenet::read.genepop(dataGen)
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} else {
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out <- adegenet::read.genepop(data)
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}
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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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# TODO: add handleData(out) or some other post-processing of data
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}
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