R/fct_selection_to_ngl.R

In nvelden/shinyNGLVieweR: Shiny application for the NGLVieweR package

#' Selection to NGL query
#'
#' @description
#' Transform sequence input to NGL query
#'
#' @param sequence Protein sequence in string format
#' @param input NGL query
#' 
#' @examples 
#' selection_to_ngl("ALAAGSDFG", "1-5 OR <DFG>")
#' @import stringr
#' @importFrom dplyr case_when
#' @export
selection_to_ngl <- function(sequence, input){
  
  #Get matches
  strings <- stringr::str_extract_all(input, "(?<=\\<)(.*?)(?=\\>)", simplify = TRUE)[1,]
  #Return input if no match
  if(length(strings) == 0 || nchar(strings) == 0){
    return(input)
  } else {
    
    #Find positions
    matchPositions <- stringr::str_locate_all(sequence, strings)
    matchPositions <- do.call(rbind, matchPositions)
    if(nrow(matchPositions) == 0){
      return(NULL)
    }
    matchPositions <- data.frame(matchPositions)
    matchPositions <- matchPositions %>%
      mutate_at(vars(.data$start, .data$end), as.character) %>%
      mutate(
        sequence = dplyr::case_when(
          start != end ~ paste(start,"-",end, sep = ""),
          TRUE ~start
        )
      )
    matchPositions <- paste(matchPositions$sequence, collapse=" OR ")
    
    input <- stringr::str_replace(input, "(?<=\\<)(.*?)(?=\\>)", matchPositions)
    input <- stringr::str_replace_all(input, "\\<|\\>", "")
    
    #Replace matches with positions in input
    return(input)
  }
}