Rather than truly random synthesis, there are semi-random barcode libraries that adhere to a given structure (e.g. clonTracer). In such cases, the ability to provide constrained barcode templates could be convenient.
Of course, the user could just generate them themselves and feed them to choices in the appropriate function with something like:
library(Biostrings)
iupac_codes <- list(
A = "A", C = "C", G = "G", T = "T",
R = c("A", "G"), Y = c("C", "T"), S = c("G", "C"),
W = c("A", "T"), K = c("G", "T"), M = c("A", "C"),
B = c("C", "G", "T"), D = c("A", "G", "T"), H = c("A", "C", "T"),
V = c("A", "C", "G"), N = c("A", "C", "G", "T")
)
generate_possible_barcodes <- function(dna_string) {
expand_char <- function(char) {
iupac_codes[[toupper(char)]]
}
chars <- strsplit(dna_string, split = "")[[1]]
possible_sequences_list <- lapply(chars, expand_char)
sequences <- expand.grid(possible_sequences_list, stringsAsFactors = FALSE)
sequences_str <- do.call(paste0, sequences)
return(sequences_str)
}
sequences <- generate_possible_barcodes("ACTGWSWSWSAA")
print(sequences)
[1] "ACTGAGAGAGAA" "ACTGTGAGAGAA" "ACTGACAGAGAA" "ACTGTCAGAGAA" "ACTGAGTGAGAA" "ACTGTGTGAGAA" "ACTGACTGAGAA" "ACTGTCTGAGAA" "ACTGAGACAGAA"
[10] "ACTGTGACAGAA" "ACTGACACAGAA" "ACTGTCACAGAA" "ACTGAGTCAGAA" "ACTGTGTCAGAA" "ACTGACTCAGAA" "ACTGTCTCAGAA" "ACTGAGAGTGAA" "ACTGTGAGTGAA"
[19] "ACTGACAGTGAA" "ACTGTCAGTGAA" "ACTGAGTGTGAA" "ACTGTGTGTGAA" "ACTGACTGTGAA" "ACTGTCTGTGAA" "ACTGAGACTGAA" "ACTGTGACTGAA" "ACTGACACTGAA"
[28] "ACTGTCACTGAA" "ACTGAGTCTGAA" "ACTGTGTCTGAA" "ACTGACTCTGAA" "ACTGTCTCTGAA" "ACTGAGAGACAA" "ACTGTGAGACAA" "ACTGACAGACAA" "ACTGTCAGACAA"
[37] "ACTGAGTGACAA" "ACTGTGTGACAA" "ACTGACTGACAA" "ACTGTCTGACAA" "ACTGAGACACAA" "ACTGTGACACAA" "ACTGACACACAA" "ACTGTCACACAA" "ACTGAGTCACAA"
[46] "ACTGTGTCACAA" "ACTGACTCACAA" "ACTGTCTCACAA" "ACTGAGAGTCAA" "ACTGTGAGTCAA" "ACTGACAGTCAA" "ACTGTCAGTCAA" "ACTGAGTGTCAA" "ACTGTGTGTCAA"
[55] "ACTGACTGTCAA" "ACTGTCTGTCAA" "ACTGAGACTCAA" "ACTGTGACTCAA" "ACTGACACTCAA" "ACTGTCACTCAA" "ACTGAGTCTCAA" "ACTGTGTCTCAA" "ACTGACTCTCAA"
[64] "ACTGTCTCTCAA"But what's the fun in that, really? Probably simpler ways to do it, I am not great with Biostrings.
Rather than truly random synthesis, there are semi-random barcode libraries that adhere to a given structure (e.g. clonTracer). In such cases, the ability to provide constrained barcode templates could be convenient.
Of course, the user could just generate them themselves and feed them to
choicesin the appropriate function with something like:But what's the fun in that, really? Probably simpler ways to do it, I am not great with
Biostrings.