R/extractEMBOSS_StartEnd.R

In currocam/FascinRSCA: R and Python code for SCA with fascin protein

#' A function to subset fasta sequence from EMBOSS raw tsv.
#'
#' @param Start A numeric vector with Start positions
#' @param End A numeric vector with End positions
#' @param seqs  A character vector containing fasta sequences
#'
#' @return It returns a character vector containing with the extracted sequence.
#' @export

extractEMBOSS_StartEnd <- function(Start, End, seqs){
  ## Check arguments
  if(!is.character(seqs))
    stop("'seqs' should be character")
  if(!is.character(Start))
    stop("'Start' should be numeric")
  if(!is.character(End))
    stop("'End' should be numeric")
  if(list(Start, End, seqs) %>%
     lengths() %>% unique() %>%
     length()!= 1)
    stop("Start, End and seqs should have the same length")

  purrr::pmap_chr(list(Start, End, seqs),
    function(n_start, n_end, seq){
      seq %>%
        seqinr::s2c() %>%
        magrittr::extract(n_start:n_end) %>%
        seqinr::c2s()
    })
}