R/read_pairs.R

In brandonsie/phipmake: PhIP-seq Data Analysis Pipeline

#' Read blast alignment pair files based on library names and metadata path.
#'
#' @param libs Character vector of library names.
#' @param pairs_path Metadata directory as character string.
#'
#' @return phiplist of blast pairs First element is character vector of
#' libraries from libs input. Remaining elements are corresponding alignment
#' files.
#'
#' @export



read_pairs_list <- function(libs, pairs_path){
  # prep output data list
  output_data <- list()

  for(i in 1:length(libs)){
    output_data[[i]] <- read_pairs(libs[i], pairs_path)
  }

  names(output_data) <- libs
  return(output_data)

}

#' Read BLAST pairs file based on md path and library name.
#'
#' @param libname Library name.
#' @param pairs_path Pairs data directory.
#'
#' @export
#'

read_pairs <- function(libname, pairs_path, pairs_grep = "_trimmedpairs"){
  #prepare to load intrapeptide alignment pairs for specific library
  # print(paste("libname:", libname))
  # print(paste("pairs path:", pairs_path))
  pairs_files <- list.files(pairs_path)

  # specify annotation file path
  lib_pairs_name <- pairs_files[grep(libname,pairs_files)] %>% min
  # print(paste("lib_pairs_name", lib_pairs_name))
  lib_pairs_path <- paste(pairs_path, lib_pairs_name, sep = "/")
  # print(paste("lib pairs path", lib_pairs_path))

  lib_pairs_files <- list.files(lib_pairs_path)
  # print(paste("lib pairs files", lib_pairs_files))
  lib_pairs_names <- lib_pairs_files[intersect(
    grep(libname,lib_pairs_files), grep(pairs_grep, lib_pairs_files))]
  # print(paste("lib pairs name", lib_pairs_names))

  lib_pairs_file_path <- paste(lib_pairs_path, lib_pairs_names, sep = "/")
  # print(paste("lib pairs file path", lib_pairs_file_path))

  annot <- data.table::fread(lib_pairs_file_path, data.table = FALSE)
  return(annot)

}