#' This function creates a scoring matrix for aligning IUPAC sequences
makeIUPACScoreMat <- function()
{
lets <- list(
U = "T",
A = "A",
C = "C",
M = c("A", "C"),
G = "G",
R = c("A", "G"),
S = c("G", "C"),
V = c("A", "C", "G"),
T = "T",
W = c("A", "T"),
Y = c("C", "T"),
H = c("A", "C", "T"),
K = c("G", "T"),
D = c("A", "G", "T"),
B = c("C", "G", "T"),
N = c("A", "C", "G", "T")
)
cat(" ")
for (i in names(lets)){
cat(" ")
cat(i)
}
cat("\n")
for (i in names(lets)){
cat(" ")
cat(i)
for (j in names(lets)){
ilets <- c(lets[[i]], i)
jlets <- c(lets[[j]], j)
any_match <- any(ilets %in% jlets) | any(jlets %in% ilets)
cat(ifelse(any_match, " 1,", " 0,"))
}
cat("\n")
}
}
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