Export the data to FASTQ files

shell.nix

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

src/repertoire.r

@@ -1,4 +1,5 @@
 library(immuneSIM)
+library(Biostrings)
 
 generate_repertoires <- function(number_of_sequences) {
   a_chain <- immuneSIM(
@@ -18,6 +19,27 @@ 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) {
@@ -29,3 +51,5 @@ 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)