From d2e45bc00fb9dca232cbfc784c39033df0447c6f Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Tue, 2 Mar 2021 20:08:14 +0100
Subject: [PATCH] Change output format to FASTA

---
 .gitignore       |  2 +-
 src/repertoire.r | 15 +++++++--------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index ec996fb..2447fda 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,2 @@
 *.txt
-*.fastq
+*.fasta
diff --git a/src/repertoire.r b/src/repertoire.r
index 0650f87..9cb5147 100644
--- a/src/repertoire.r
+++ b/src/repertoire.r
@@ -1,7 +1,7 @@
 library(immuneSIM)
 library(Biostrings)
 
-generate_repertoires <- function(number_of_sequences) {
+generate_repertoire <- function(number_of_sequences) {
   b_chain <- immuneSIM(
     number_of_seqs = number_of_sequences,
     species = "hs",
@@ -22,9 +22,8 @@ preprocess_data <- function(repertoire, sequencing_runs) {
 }
 
 save_data <- function(repertoire) {
-  file_name <- "data/sequence.fastq"
-  # TODO Change format to fasta
-  Biostrings::writeXStringSet(repertoire, file_name, format = "fastq")
+  file_name <- "data/sequence.fasta"
+  Biostrings::writeXStringSet(repertoire, file_name, format = "fasta")
 }
 
 parse_cli_arguments <- function(args) {
@@ -35,9 +34,9 @@ parse_cli_arguments <- function(args) {
 }
 
 args <- commandArgs(trailingOnly = TRUE)
-parameters <- parse_cli_arguments(args)
-number_of_sequences <- as.integer(parameters[1])
-sequencing_runs <- as.integer(parameters[2])
-repertoire <- generate_repertoires(number_of_sequences)
+arguments <- parse_cli_arguments(args)
+number_of_sequences <- as.integer(arguments[1])
+sequencing_runs <- as.integer(arguments[2])
+repertoire <- generate_repertoire(number_of_sequences)
 processed_data <- preprocess_data(repertoire, sequencing_runs)
 save_data(processed_data)
\ No newline at end of file