#' Write random sequences to fasta file

#' 

#' Create random sequences from predefined vocabulary and write to fasta file.

#' 

#' @param file_path Output directory; can also be a file name but only possible if \code{write_to_file_path = TRUE} and 

#' \code{num_files = 1}).

#' @param num_files Number of files to create.

#' @param header Fasta header name. 

#' @param seq_length Length of one sequence. If vector longer than 1, will randomly sample from that vector. 

#' @param num_seq Number of sequences per file.

#' @param fasta_name_start Beginning string of file name. Output files are named fasta_name_start + _i.fasta where i is an integer index.

#' @param write_to_file_path Whether to write output directly to \code{file_path}, i.e. file_path is not a directory.

#' @param prob Probability of each character in the \code{vocabulary} to be sampled. If `NULL` each character has same probability.

#' @param vocabulary Set of characters to sample sequences from. 

#' @examples

#' path_output <- tempfile()

#' dir.create(path_output)

#' create_dummy_data(file_path = path_output,

#'                   num_files = 3,

#'                   seq_length = 11, 

#'                   num_seq = 5,                   

#'                   vocabulary = c("a", "c", "g", "t"))

#' list.files(path_output)                

#'    

#' @returns None. Writes data to files.     

#' @export

create_dummy_data <- function(file_path,

                              num_files,

                              header = "header", 

                              seq_length, 

                              num_seq,

                              fasta_name_start = "file",

                              write_to_file_path = FALSE,

                              prob = NULL,

                              vocabulary = c("a", "c", "g", "t")) {

  if (!is.null(prob)) {

    stopifnot(length(prob) == length(vocabulary))

    stopifnot(abs(1 - sum(prob)) < 1e-10)

  }

  if (write_to_file_path) {

    stopifnot(num_files == 1)

  }

  if (!dir.exists(file_path) & !write_to_file_path) {

    dir.create(file_path)

  }

  for (i in 1:num_files){

    df <- data.frame(Header = NULL, Sequence = NULL)

    for (j in 1:num_seq) {

      nuc_seq <- random_seq(vocabulary = vocabulary, seq_length = seq_length, prob = prob)

      new_row <- data.frame(Header = header, Sequence = nuc_seq)

      df <- rbind(df, new_row)

    }

    df$Header <- as.character(df$Header)

    df$Sequence <- as.character(df$Sequence)

    if (write_to_file_path) {

      out.file <- file_path

    } else {

      file_name <- paste0(fasta_name_start, "_", i, ".fasta")

      out.file <- file.path(file_path, file_name)

    }

    microseq::writeFasta(fdta = dplyr::as_tibble(df), 

                         out.file =  out.file)

  }

}

random_seq <- function(vocabulary, seq_length, prob = NULL) {

  if (length(seq_length) > 1) {

    seq_length <- sample(seq_length, 1)

  }

  sample(vocabulary, seq_length, replace = TRUE, prob = prob) %>% paste(collapse = "")

}