R/read_gbk.R

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

#' Read genbank files
#'
#' Genbank flat files (.gb/.gbk/.gbff) and their ENA and DDBJ equivalents have a
#' particularly gruesome format. That's why [read_gbk()] is just a wrapper
#' around a Perl-based `gb2gff` converter and [read_gff3()].
#'
#' @importFrom readr read_tsv
#' @inheritParams read_gff3
#' @export
#' @return tibble
read_gbk <- function(file, sources=NULL, types=NULL, infer_cds_parents=TRUE){

  gb2gff <- base::system.file("exec/gb2gff", package="gggenomes")

  if(file_is_zip(file) && file_ext(file, ignore_zip = FALSE) != "gz")
    abort(str_glue("Decompressing for genbank only works with gzipped files, not `{suf}`"))

  if(file_is_url(file) && file_is_zip(file)){
    file <- pipe(str_glue("curl {file} | gzip -cd | {gb2gff} -S"))
  }else if(file_is_url(file)){
    file <- pipe(str_glue("curl {file} | {gb2gff} -S"))
  }else if(file_is_zip(file)){
    suf <- file_ext(file, ignore_zip = FALSE)
    if(suf != "gz")
      abort(str_glue("Decompressing for genbank only works with gzipped files, not `{suf}`"))
    file <- pipe(str_glue("gzip -cd {file} | {gb2gff} -S"))
  }else{
    file <- pipe(str_glue("{gb2gff} -S {file}"))
  }

  read_gff3(file, sources=sources, types=types,
    infer_cds_parents=infer_cds_parents)
}