src/alignment.r

@@ -11,13 +11,6 @@ parse_data <- function(file) {
   return(list(sequences, vj_segments))
 }
 
-parse_metadata <- function(metadata) {
-  id_elements <- unlist(strsplit(metadata, split = " "))
-  v_identifier <- id_elements[2]
-  j_identifier <- id_elements[3]
-  return(list(v_id = v_identifier, j_id = j_identifier))
-}
-
 match_id_sequence <- function(names, vdj_segments, id) {
   matches <- grep(names, pattern = id)
   row <- matches[1]
@@ -25,20 +18,22 @@ match_id_sequence <- function(names, vdj_segments, id) {
 }
 
 get_vj_sequence <- function(metadata, names, vdj_segments) {
-  identifiers <- parse_metadata(metadata)
-  v_sequence <- match_id_sequence(names, vdj_segments, id = identifiers["v_id"])
-  j_sequence <- match_id_sequence(names, vdj_segments, id = identifiers["j_id"])
-  return(list(v_seq = v_sequence, j_seq = j_sequence))
+  id_elements <- unlist(strsplit(metadata, split = " "))
+  v_identifier <- id_elements[2]
+  j_identifier <- id_elements[3]
+  v_sequence <- match_id_sequence(names, vdj_segments, id = v_identifier)
+  j_sequence <- match_id_sequence(names, vdj_segments, id = j_identifier)
+  return(c(v_sequence, j_sequence))
 }
 
 fetch_vj_sequences <- function(sequences, vdj_segments) {
-  vj_sequences <- sapply(names(sequences),
+  vj_sequences <- mclapply(names(sequences),
     names(vdj_segments),
     vdj_segments,
-    FUN = get_vj_sequence
+    FUN = get_vj_sequence,
+    mc.cores = detectCores()
   )
-  results <- data.frame(t(vj_sequences))
-  return(results)
+  return(c(vj_sequences[1], vj_sequences[2]))
 }
 
 align_sequence <- function(sequence, vdj_segment) {
@@ -52,10 +47,15 @@ align_sequence <- function(sequence, vdj_segment) {
 
 # TODO Extract CDR3
 get_hvr_sequences <- function(sequences, vdj_segments) {
-  df <- fetch_vj_sequences(sequences, vdj_segments)
-  v_alignment <- parallel::mcmapply(sequences, df$v_seq, FUN = align_sequence)
-  j_alignment <- parallel::mcmapply(sequences, df$j_seq, FUN = align_sequence)
-  print(v_alignment)
+  vj_sequences <- fetch_vj_sequences(sequences, vdj_segments)
+  v_alignment <- parallel::mcmapply(sequences,
+    vj_sequences[1],
+    FUN = align_sequence
+  )
+  j_alignment <- parallel::mcmapply(sequences,
+    vj_sequences[2],
+    FUN = align_sequence
+  )
 }
 
 data <- parse_data(file = "data/curesim_sequence.fastq")