|
1
|
|
# Generate a parameter file.
|
|
2
|
|
create_par_file <- function(files, data, params) {
|
|
3
|
1
|
geno <- data$geno
|
|
4
|
1
|
snp <- data$snp
|
|
5
|
1
|
ind <- ifelse(is.null(data$group), data$ind, data$group)
|
|
6
|
1
|
exclude <- data$exclude
|
|
7
|
|
|
|
8
|
1
|
sprintf("genotypename: %s\nsnpname: %s\nindivname: %s\n", geno, snp, ind) %>%
|
|
9
|
1
|
writeLines(con = files$par_file)
|
|
10
|
|
|
|
11
|
1
|
if (!is.null(files[["pop_file"]])) {
|
|
12
|
1
|
write(sprintf("popfilename: %s\n", files$pop_file), file = files$par_file, append = TRUE)
|
|
13
|
1
|
} else if (!is.null(files$popleft) & !is.null(files$popright)) {
|
|
14
|
1
|
write(sprintf("popleft: %s", files$popleft), file = files$par_file, append = TRUE)
|
|
15
|
1
|
write(sprintf("popright: %s", files$popright), file = files$par_file, append = TRUE)
|
|
16
|
|
}
|
|
17
|
|
|
|
18
|
1
|
if (!is.null(exclude)) {
|
|
19
|
1
|
write(sprintf("badsnpname: %s", exclude), file = files$par_file, append = TRUE)
|
|
20
|
|
}
|
|
21
|
|
|
|
22
|
|
# write user-specified parameters
|
|
23
|
1
|
for (par in names(params)) {
|
|
24
|
1
|
write(sprintf("%s: %s\n", par, params[[par]]), file = files$par_file, append = TRUE)
|
|
25
|
|
}
|
|
26
|
|
}
|
|
27
|
|
|
|
28
|
|
|
|
29
|
|
# Generate a file with populations for a qpF4ratio run.
|
|
30
|
|
create_qpF4ratio_pop_file <- function(X, A, B, C, O, file) {
|
|
31
|
1
|
lines <- sprintf("%s %s : %s %s :: %s %s : %s %s", A, O, X, C, A, O, B, C)
|
|
32
|
1
|
writeLines(lines, file)
|
|
33
|
|
}
|
|
34
|
|
|
|
35
|
|
|
|
36
|
|
# Generate a file with populations for a qpDstat run.
|
|
37
|
|
create_qpDstat_pop_file <- function(W = NULL, X = NULL, Y = NULL, Z = NULL, file) {
|
|
38
|
1
|
lines <- c()
|
|
39
|
1
|
for (w in W) for (x in X) for (y in Y) for (z in Z) {
|
|
40
|
1
|
lines <- c(lines, sprintf("%s %s %s %s", w, x, y, z))
|
|
41
|
|
}
|
|
42
|
1
|
writeLines(lines, file)
|
|
43
|
|
}
|
|
44
|
|
|
|
45
|
|
|
|
46
|
|
# Generate a file with populations for a qpDstat run based on given
|
|
47
|
|
# list of quartets.
|
|
48
|
|
create_qpDstat_pop_file_quartets <- function(quartets, file) {
|
|
49
|
0
|
lines <- c()
|
|
50
|
0
|
for (q in quartets) {
|
|
51
|
0
|
lines <- c(lines, sprintf("%s %s %s %s", q[1], q[2], q[3], q[4]))
|
|
52
|
|
}
|
|
53
|
0
|
writeLines(lines, file)
|
|
54
|
|
}
|
|
55
|
|
|
|
56
|
|
|
|
57
|
|
# Generate a file with populations for a qp3Pop run.
|
|
58
|
|
create_qp3Pop_pop_file <- function(A, B, C, file) {
|
|
59
|
1
|
lines <- c()
|
|
60
|
1
|
for (a in A) for (b in B) for (c in C) {
|
|
61
|
1
|
lines <- c(lines, sprintf("%s %s %s", a, b, c))
|
|
62
|
|
}
|
|
63
|
1
|
writeLines(lines, file)
|
|
64
|
|
}
|
|
65
|
|
|
|
66
|
|
# Generate a file with populations for a qpDstat run.
|
|
67
|
|
create_leftright_pop_files <- function(left, right, files) {
|
|
68
|
1
|
writeLines(left, files$popleft)
|
|
69
|
1
|
writeLines(right, files$popright)
|
|
70
|
|
}
|
|
71
|
|
|
bodkan