From 81ebd4fbbefda50a07fb9a11ce7a48ab55cc464c Mon Sep 17 00:00:00 2001 From: coolneng Date: Wed, 21 Apr 2021 22:12:29 +0200 Subject: [PATCH] Rename function arguments to improve readability --- src/alignment.r | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/alignment.r b/src/alignment.r index 7175e86..63b161a 100644 --- a/src/alignment.r +++ b/src/alignment.r @@ -11,22 +11,22 @@ parse_data <- function(file) { return(list(sequences, vj_segments)) } -match_id_sequence <- function(names, sequences, id) { +match_id_sequence <- function(names, vdj_segments, id) { matches <- grep(names, pattern = id) row <- matches[1] - return(as.character(sequences[row])) + return(as.character(vdj_segments[row])) } -get_vj_sequence <- function(sequences, names, vdj_segments) { - metadata <- unlist(strsplit(sequences, split = " ")) - v_identifier <- metadata[2] - j_identifier <- metadata[3] +get_vj_sequence <- function(metadata, names, vdj_segments) { + 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(vdj_segments, sequences) { +fetch_vj_sequences <- function(sequences, vdj_segments) { vj_sequences <- mclapply(names(sequences), names(vdj_segments), vdj_segments, @@ -45,8 +45,9 @@ align_sequence <- function(sequence, vdj_segment) { )) } +# TODO Extract CDR3 get_hvr_sequences <- function(sequences, vdj_segments) { - vj_sequences <- fetch_vj_sequences(vdj_segments, sequences) + vj_sequences <- fetch_vj_sequences(sequences, vdj_segments) v_alignment <- parallel::mcmapply(sequences, vj_sequences[1], FUN = align_sequence