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locigenesis
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Save vdj alignment sequences to a CSV

This commit is contained in:
coolneng 2021-03-23 19:33:32 +01:00
parent 97b8914cd5
commit 66b39485a9
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
2 changed files with 15 additions and 13 deletions
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2
.gitignore vendored
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@ -1,3 +1,3 @@
*.txt
*.csv
*.fasta
*.fastq

26
src/repertoire.r
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@ -19,21 +19,23 @@ amplify_rows <- function(data, column, factor) {
return(rep(data, factor))
}
save_data <- function(data, name) {
if (name == "sequence") {
file_name <- paste("data/", name, ".fasta", sep = "")
Biostrings::writeXStringSet(data, file_name, format = "fasta")
} else {
file_name <- paste("data/", name, ".txt", sep = "")
cat(data, file = file_name, sep = "\n")
}
save_data <- function(data) {
Biostrings::writeXStringSet(data$sequence, "data/sequence.fasta")
vdj_sequences <- data[-1]
write.csv(vdj_sequences, "data/vdj_alignment.csv", row.names = FALSE)
}
process_data <- function(repertoire, sequencing_runs) {
columns <- c("sequence", "v_call", "j_call")
columns <- c(
"sequence", "v_sequence_alignment",
"d_sequence_alignment", "j_sequence_alignment"
)
data <- repertoire[, columns]
amplified_data <- mapply(data, names(data), sequencing_runs, FUN = amplify_rows)
invisible(mapply(amplified_data, names(amplified_data), FUN = save_data))
amplified_data <- mapply(data, names(data),
sequencing_runs,
FUN = amplify_rows
)
save_data(amplified_data)
}
parse_cli_arguments <- function(args) {
@ -48,4 +50,4 @@ arguments <- parse_cli_arguments(args)
number_of_sequences <- as.integer(arguments[1])
sequencing_runs <- as.integer(arguments[2])
repertoire <- generate_repertoire(number_of_sequences)
process_data(repertoire, sequencing_runs)
process_data(repertoire, sequencing_runs)