Add function to load .bed files

.Rbuildignore

@@ -2,6 +2,7 @@
 ^fasta_files$
 ^genbank_files$
 ^gff_files$
+^bed_files$
 ^renv$
 ^renv\.lock$
 ^.*\.Rproj$

.gitignore

@@ -6,6 +6,7 @@
 .DS_store
 renv/
 fasta_files/
+bed_files/
 genbank_files/
 gff_files/
 renv.lock

NAMESPACE

@@ -24,6 +24,7 @@ export(GC_tooltip)
 export(GC_trackMouse)
 export(gbk_features_to_df)
 export(protein_blast)
+export(read_bed)
 export(read_fasta)
 export(read_gbk)
 export(read_gff)

R/read_bed.R

@@ -0,0 +1,130 @@
+#' Read BED Files
+#'
+#' This function reads BED files from a specified directory or file path and
+#' combines them into a single data frame. BED files use 0-based coordinate starts,
+#' while this function transforms the coordinates to 1-based during import.
+#'
+#' @param path A character string specifying the directory containing BED files
+#'   or the file path to a single BED file.
+#'
+#' @return A data frame combining data from the BED files.
+#'
+#' @details This function can read multiple BED files from a directory or a
+#'   single BED file from a specified path. It adds a 'filename' column with the
+#'   name of the file, and combines the data frames from all files into one.
+#'
+#' @examples
+#' \dontrun{
+#' # Read BED files from a directory
+#' bed_data <- read_bed("path/to/directory")
+#'
+#' # Read a single BED file
+#' bed_data <- read_bed("path/to/file.bed")
+#' }
+#' @importFrom dplyr bind_rows
+#' @export
+read_bed <- function(path){
+
+  if(dir.exists(path)){
+    # It's a directory
+    files <- list.files(path, pattern = "\\.bed[0-9]*$", full.names = TRUE)
+
+    # Check if there are any .bed files in the directory
+    if (length(files) == 0) {
+      stop("No .bed files found in the specified directory.")
+    }
+
+    # Initialize an empty list to store data frames from each file
+    data_list <- list()
+
+    # Process each .bed file in the directory
+    for (file in files) {
+      data <- process_bed(file)
+      filename <- sub("\\.bed[0-9]*$", "", basename(file))
+      data$filename <- filename
+      data_list[[filename]] <- data
+    }
+
+    # Combine data frames from all files into one
+    combined_data <- do.call(dplyr::bind_rows, data_list)
+
+    return(combined_data)
+
+  } else if(file.exists(path)){
+
+    data <- process_bed(path)
+
+    return(data)
+
+  } else {
+    stop("The specified path does not exist.")
+  }
+}
+
+#' @noRd
+block_to_numeric <- function(x) {
+  as.numeric(unlist(strsplit(x, ","))) + 1
+}
+
+#' @noRd
+process_bed <- function(path){
+
+  field_names <- c("chrom", "chromStart", "chromEnd", "name", "score",
+                   "strand", "thickStart", "thickEnd", "itemRgb", "blockCount",
+                   "blockSizes", "blockStarts")
+
+  if(file.exists(path)){
+
+    lines <- readLines(path)
+    # Find the line with the pattern 'track'
+    track_line <- grep("track", lines)
+    # Read data from the line after the 'track' line if it exists
+    if (length(track_line) > 0) {
+      lines <- lines[(track_line + 1):length(lines)]
+    }
+
+    # Determine the number of columns from the first data line
+    if (length(lines) > 0) {
+      num_cols <- length(strsplit(lines[1], "\t")[[1]])
+      used_fields <- field_names[1:num_cols]
+    } else {
+      used_fields <- field_names
+    }
+
+    data <- read.table(
+      text = lines,
+      header = FALSE,
+      quote = "",
+      sep = "\t",
+      fill = TRUE,
+      stringsAsFactors = FALSE,
+      col.names = used_fields
+    )
+
+    # Add +1 to Start and End
+    if ("chromStart" %in% colnames(data)) {
+    data$chromStart <- data$chromStart + 1
+    }
+    if("chromEnd" %in% colnames(data)){
+    data$chromEnd <- data$chromEnd + 1
+    }
+    if ("thickStart" %in% colnames(data)) {
+      data$thickStart <- data$thickStart + 1
+    }
+    if("thickEnd" %in% colnames(data)){
+      data$thickEnd <- data$thickEnd + 1
+    }
+    # Convert blocks to numeric vector
+    if ("blockSizes" %in% colnames(data)) {
+      data$blockSizes <- sapply(data$blockSizes, block_to_numeric)
+    }
+    if ("blockStarts" %in% colnames(data)) {
+      data$blockStarts <- sapply(data$blockStarts, block_to_numeric)
+    }
+
+  } else {
+    stop("The specified path does not exist.")
+  }
+
+  return(data)
+}