From 53dda36c66b1eafce128b74f1b8f646ea79c698c Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Fri, 26 Feb 2021 02:20:11 +0100
Subject: [PATCH] Export the data to FASTQ files

---
 src/repertoire.r | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/repertoire.r b/src/repertoire.r
index 4ed9b55..b7a5d83 100644
--- a/src/repertoire.r
+++ b/src/repertoire.r
@@ -34,6 +34,12 @@ preprocess_data <- function(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) {
@@ -46,3 +52,4 @@ 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)
\ No newline at end of file