shell.nix

@@ -6,7 +6,6 @@ mkShell {
   buildInputs = [
     R
     rPackages.immuneSIM
-    rPackages.Biostrings
     jdk
     # Develoment tools
     rPackages.languageserver

src/repertoire.r

@@ -1,5 +1,4 @@
 library(immuneSIM)
-library(Biostrings)
 
 generate_repertoires <- function(number_of_sequences) {
   a_chain <- immuneSIM(
@@ -19,27 +18,6 @@ generate_repertoires <- function(number_of_sequences) {
   return(list("a_chain" = a_chain, "b_chain" = b_chain))
 }
 
-process_chain <- function(repertoire) {
-  sequences <- as.character(repertoire$sequence)
-  counts <- as.integer(repertoire$counts)
-  reads <- Biostrings::DNAStringSet(rep(sequences, counts))
-  names(reads) <- seq_len(length(reads))
-  reverse_complement <- Biostrings::reverseComplement(reads)
-  return(reverse_complement)
-}
-
-preprocess_data <- function(repertoires) {
-  filtered_repertoires <- lapply(repertoires, process_chain)
-  names(filtered_repertoires) <- names(repertoires)
-  return(filtered_repertoires)
-}
-
-save_data <- function(repertoires) {
-  for (chain in names(repertoires)) {
-    file_name <- paste("data/", chain, ".fastq", sep = "")
-    Biostrings::writeXStringSet(repertoires[[chain]], file_name, format = "fastq")
-  }
-}
 
 parse_cli_arguments <- function(args) {
   if (length(args) != 1) {
@@ -51,5 +29,3 @@ parse_cli_arguments <- function(args) {
 args <- commandArgs(trailingOnly = TRUE)
 number_of_sequences <- parse_cli_arguments(args)
 sim_repertoire <- generate_repertoires(number_of_sequences)
-processed_data <- preprocess_data(sim_repertoire)
-save_data(processed_data)