R/read.R

In arendsee/synder: Use Synteny to Filter Genomic Search

#' Synder read functions
#'
#' read synder classes from files
#'
#' @param file TAB-delimited file
#' @param ... Additional arguments for the casting function (\code{as_*})
#' @name synder_read
NULL


#' @rdname synder_read
#' @export
read_synmap <- function(file, ...) {
  readr::read_tsv(
    file,
    col_types = 'ciiciidc',
    col_names = names(SYNMAP_COLS),
    comment   = "#"
  ) %>% as_synmap(...)
}

#' @rdname synder_read
#' @export
read_gff <- function(file, ...) {
  readr::read_tsv(
    file,
    col_types = 'ccciincic',
    col_names = names(GFF_COLS),
    na        = ".",
    comment   = "#"
  ) %>% as_gff(...)
}

#' @rdname synder_read
#' @export
read_conlen <- function(file, ...) {
  readr::read_tsv(
    file,
    col_names = names(CON_LENGTH),
    col_types = 'ci',
    comment   = "#"
  ) %>% as_conlen(...)
}