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locigenesis
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Change output format to FASTA

This commit is contained in:
coolneng 2021-03-02 20:08:14 +01:00
parent deb1066982
commit d2e45bc00f
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
2 changed files with 8 additions and 9 deletions
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2
.gitignore vendored
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@ -1,2 +1,2 @@
*.txt
*.fastq
*.fasta

15
src/repertoire.r
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@ -1,7 +1,7 @@
library(immuneSIM)
library(Biostrings)
generate_repertoires <- function(number_of_sequences) {
generate_repertoire <- function(number_of_sequences) {
b_chain <- immuneSIM(
number_of_seqs = number_of_sequences,
species = "hs",
@ -22,9 +22,8 @@ preprocess_data <- function(repertoire, sequencing_runs) {
}
save_data <- function(repertoire) {
file_name <- "data/sequence.fastq"
# TODO Change format to fasta
Biostrings::writeXStringSet(repertoire, file_name, format = "fastq")
file_name <- "data/sequence.fasta"
Biostrings::writeXStringSet(repertoire, file_name, format = "fasta")
}
parse_cli_arguments <- function(args) {
@ -35,9 +34,9 @@ parse_cli_arguments <- function(args) {
}
args <- commandArgs(trailingOnly = TRUE)
parameters <- parse_cli_arguments(args)
number_of_sequences <- as.integer(parameters[1])
sequencing_runs <- as.integer(parameters[2])
repertoire <- generate_repertoires(number_of_sequences)
arguments <- parse_cli_arguments(args)
number_of_sequences <- as.integer(arguments[1])
sequencing_runs <- as.integer(arguments[2])
repertoire <- generate_repertoire(number_of_sequences)
processed_data <- preprocess_data(repertoire, sequencing_runs)
save_data(processed_data)