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Save vj_sequences in a dataframe

This commit is contained in:
coolneng 2021-04-22 01:18:25 +02:00
parent a7c1df5ce2
commit 83819b296b
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
1 changed files with 8 additions and 13 deletions
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21
src/alignment.r
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@ -32,13 +32,13 @@ get_vj_sequence <- function(metadata, names, vdj_segments) {
} }
fetch_vj_sequences <- function(sequences, vdj_segments) { fetch_vj_sequences <- function(sequences, vdj_segments) {
vj_sequences <- mclapply(names(sequences), vj_sequences <- sapply(names(sequences),
names(vdj_segments), names(vdj_segments),
vdj_segments, vdj_segments,
FUN = get_vj_sequence, FUN = get_vj_sequence
mc.cores = detectCores()
) )
return(c(vj_sequences[1], vj_sequences[2])) results <- data.frame(t(vj_sequences))
return(results)
} }
align_sequence <- function(sequence, vdj_segment) { align_sequence <- function(sequence, vdj_segment) {
@ -52,15 +52,10 @@ align_sequence <- function(sequence, vdj_segment) {
# TODO Extract CDR3 # TODO Extract CDR3
get_hvr_sequences <- function(sequences, vdj_segments) { get_hvr_sequences <- function(sequences, vdj_segments) {
vj_sequences <- fetch_vj_sequences(sequences, vdj_segments) df <- fetch_vj_sequences(sequences, vdj_segments)
v_alignment <- parallel::mcmapply(sequences, v_alignment <- parallel::mcmapply(sequences, df$v_seq, FUN = align_sequence)
vj_sequences[1], j_alignment <- parallel::mcmapply(sequences, df$j_seq, FUN = align_sequence)
FUN = align_sequence print(v_alignment)
)
j_alignment <- parallel::mcmapply(sequences,
vj_sequences[2],
FUN = align_sequence
)
} }
data <- parse_data(file = "data/curesim_sequence.fastq") data <- parse_data(file = "data/curesim_sequence.fastq")