Add v_call and j_call to sequence ID

src/repertoire.r

@@ -10,19 +10,13 @@ generate_repertoire <- function(number_of_sequences) {
   ))
 }
 
-save_data <- function(data, reads) {
-  Biostrings::writeXStringSet(data$sequence, "data/sequence.fasta")
-  vdj_sequences <- data[-1]
-  amplified_vdj <- vdj_sequences[rep(seq_len(nrow(vdj_sequences)), reads), ]
-  write.csv(amplified_vdj, "data/vdj_metadata.csv", row.names = FALSE)
-}
-
 process_data <- function(repertoire, reads) {
-  columns <- c("sequence", "junction", "v_call", "j_call")
+  columns <- c("sequence", "v_call", "j_call")
   data <- repertoire[, columns]
   dna_sequence <- Biostrings::DNAStringSet(data$sequence)
   data$sequence <- Biostrings::reverseComplement(dna_sequence)
-  save_data(data, reads)
+  names(data$sequence) <- paste(rownames(data), data$v_call, data$j_call)
+  Biostrings::writeXStringSet(data$sequence, "data/sequence.fasta")
 }
 
 parse_cli_arguments <- function() {