R/msa.R

In philliplab/EpitopeMatcher: Epitope Matcher

#' @include patient_HLA.R
NULL

#' Reads in the query alignment
#'
#' This function currently just calls readAAStringSet in the Biostrings
#' package. See that function for more details.
#'
#' Must be a valid FASTA file.
#'
#' The FASTA headers must be in some delimited form with a special character
#' used for delimiting different fields. Further more, the patient id must
#' always be in the same column in the FASTA header. For example:
#' PATID_TIME_PID_CONSENSUSDETAILS
#'
#' @param file_name Name of the fasta file
#' @export

read_query_alignment <- function(file_name){
  x <- readAAStringSet(file_name)
  return(x)
}

#' A function that returns a test query alignment
#' @param dataset_name The name of the test dataset to return
#' @export

get_test_query_alignment <- function(dataset_name = 'base'){
  data_sets <- list(
    'base' =  AAStringSet(structure(c(
        "MGARASVLSGGELDRWEKIRLRPGGKK-YKLKHIVWASRELERFAVNPPPPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVAT", 
        "MGTRASVLSGIEADRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNP---GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVAT", 
        "MGARASVLSGGEADRREKIRLRPGGKKKYKLKHIVWASRELERFAVNPPPPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVAT", 
        "MGTRASVLSQGEADRREKQRLRPGGKKKYKLKHIVWASRELERFAVNPPPPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVAT"), 
      .Names = c("hxb2 ", "pat01|scribbles", 
                 "pat02|human|protein piece|>@booo \"\" -/.,!@#@#%^&*()", "pat03")))
  )
  return(data_sets[[dataset_name]])
}

#' @rdname get_patient_ids-methods
#' @aliases get_patient_ids
setMethod("get_patient_ids", "AAStringSet",
          function(x, sep = '\\|', id_position = 1){
            if (is.null(sep) | is.null(id_position)){
              return (names(x))
            } else {
              split_names <- strsplit(names(x), sep)
              names_vector <- unlist(lapply(split_names, `[[`, id_position))
              names_vector <- gsub("^ +", "", names_vector)
              names_vector <- gsub(" +$", "", names_vector)
              return(names_vector)
            }
          })