R/table_to_fasta.R

In Hide-Fun/teco:

#' Convert table to fasta.
#'
#' @param .data data.frame
#' @param .otu otu column name.
#' @param .seq sequence column name.
#' @export
#' @examples
#'
#' library(tibble)
#'
#' table <-
#'    tibble(otu = c("otu_1", "otu_2"),
#'           seq = c("ATGGG", "GCCGTA"))
#'
#' table_to_fasta(.data = table, .otu = otu, .seq = seq)
#'
table_to_fasta <- function(.data, .otu, .seq) {
  otu <- dplyr::enquo(.otu)
  seq <- dplyr::enquo(.seq)
  # select
  n <- nrow(.data)
  otu_col <- .data %>%
    dplyr::select(!!otu) %>%
    dplyr::rename(col = !!otu) %>%
    dplyr::mutate(col = stringr::str_c(">", col)) %>%
    tibble::add_column(num = seq(1, 2 * n, by = 2))
  seq_col <- .data %>%
    dplyr::select(!!seq) %>%
    dplyr::rename(col = !!seq) %>%
    tibble::add_column(num = seq(1, 2 * n, by = 2) + 1)
  # bind
  fasta <- dplyr::bind_rows(otu_col, seq_col) %>%
    dplyr::arrange(num) %>%
    dplyr::select(col)
  return(fasta)
}