tests/testthat/test_BKtree_utils.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
test_that("levenshtein_distance() works", {
# ground truth e.g. from:
# stringdist::stringdist(s1, s2, method = "lv")
s1 <- "AAAAAAACCC"
s2 <- "AAAAAACCCC"
s3 <- "ACGTACGTACGT"
s4 <- "CGTACGTACGTA"
expect_error(levenshtein_distance(c(s1, s1), s2))
expect_error(levenshtein_distance(s1, c(s2, s2)))
expect_identical(levenshtein_distance(s1, s1), 0L)
expect_identical(levenshtein_distance(s2, s2), 0L)
expect_identical(levenshtein_distance(s3, s3), 0L)
expect_identical(levenshtein_distance(s4, s4), 0L)
expect_identical(levenshtein_distance(s1, s2), 1L)
expect_identical(levenshtein_distance(s1, s3), 8L)
expect_identical(levenshtein_distance(s1, s4), 9L)
expect_identical(levenshtein_distance(s2, s3), 9L)
expect_identical(levenshtein_distance(s2, s4), 9L)
expect_identical(levenshtein_distance(s3, s4), 2L)
})
test_that("hamming_distance() works", {
# ground truth e.g. from:
# stringdist::stringdist(s1, s2, method = "hamming")
s1 <- "AAAAAAACCC"
s2 <- "AAAAAACCCC"
s3 <- "ACGTACGTACGT"
s4 <- "CGTACGTACGTA"
expect_error(hamming_distance(c(s1, s1), s2))
expect_error(hamming_distance(s1, c(s2, s2)))
expect_identical(hamming_distance(s1, s1), 0L)
expect_identical(hamming_distance(s2, s2), 0L)
expect_identical(hamming_distance(s3, s3), 0L)
expect_identical(hamming_distance(s4, s4), 0L)
expect_identical(hamming_distance(s1, s2), 1L)
expect_identical(hamming_distance(s2, s1), 1L)
expect_identical(hamming_distance(s3, s4), 12L)
expect_identical(hamming_distance(s4, s3), 12L)
})
test_that("hamming_shift_distance() works", {
# ground truth e.g. from:
# s <- 1; stringdist::stringdist(substr(s1, 1, 15 - s), substr(s2, 1 + s, 15), "hamming") + 2 * s
# s <- 1; stringdist::stringdist(substr(s2, 1, 15 - s), substr(s1, 1 + s, 15), "hamming") + 2 * s
s1 <- "AAACAAAACGTTGCC"
s2 <- "ACAAAACGTTGCCCC"
s3 <- "AGTCATGCTTAGAAA"
s4 <- "AAAAGTCATGCTTAG"
expect_error(hamming_shift_distance(c(s1, s1), s2))
expect_error(hamming_shift_distance(s1, c(s2, s2)))
expect_error(hamming_shift_distance(s1, s2, c(1L, -1L)))
expect_identical(hamming_shift_distance(s1, s1), 0L)
expect_identical(hamming_shift_distance(s2, s2), 0L)
expect_identical(hamming_shift_distance(s3, s3), 0L)
expect_identical(hamming_shift_distance(s4, s4), 0L)
expect_identical(hamming_shift_distance(s1, s2, 0), 9L)
expect_identical(hamming_shift_distance(s1, s2, 1), 9L)
expect_identical(hamming_shift_distance(s1, s2, 2), 4L)
expect_identical(hamming_shift_distance(s1, s2, 3), 4L)
expect_identical(hamming_shift_distance(s1, s2, -1), 4L)
expect_identical(hamming_shift_distance(s3, s4, 0), 11L)
expect_identical(hamming_shift_distance(s3, s4, 1), 11L)
expect_identical(hamming_shift_distance(s3, s4, 2), 11L)
expect_identical(hamming_shift_distance(s3, s4, 3), 6L)
expect_identical(hamming_shift_distance(s3, s4, -1), 6L)
})
# using Rcpp-module that exposes the BKtree class to R
test_that("low-level BKtree wrapper functions work as expected", {
# create random k-mers
set.seed(42)
k <- 30L
n <- 20
alph <- c("A","C","G","T","N")
seqs <- unlist(lapply(seq_len(n - length(alph) + 1),
function(i) paste(sample(alph, size = k, replace = TRUE),
collapse = "")))
seqs <- c(seqs, paste0(setdiff(alph, substr(seqs[1], 1, 1)),
substr(seqs[1], 2, k)))
# load module and create tree instances
bk <- Rcpp::Module("mod_BKtree", PACKAGE = "mutscan")
BKtree <- bk$BKtree
expect_error(new(BKtree, "error"))
# expect_error(new(BKtree, seqs, "error")) # triggers an unrecoverable crash in BioC 3.17 -> deactivate
expect_error(new(BKtree, seqs, "hamming_shift", c(1L, -1L)))
tree <- new(BKtree)
tree2 <- new(BKtree, "levenshtein")
tree3 <- new(BKtree, seqs[c(seq.int(n), seq.int(n))], "hamming", -1)
tree4 <- new(BKtree, character(0), "hamming", -1)
tree5 <- new(BKtree, "hamming_shift", 5L)
tree6 <- new(BKtree, "hamming_shift", 0L)
expect_s4_class(bk, "Module")
expect_s4_class(BKtree, "C++Class")
expect_s4_class(tree, "Rcpp_BKtree")
expect_s4_class(tree2, "Rcpp_BKtree")
expect_s4_class(tree3, "Rcpp_BKtree")
expect_s4_class(tree4, "Rcpp_BKtree")
expect_s4_class(tree5, "Rcpp_BKtree")
expect_s4_class(tree6, "Rcpp_BKtree")
expect_identical(tree$distance_metric(), "hamming")
expect_identical(tree2$distance_metric(), "levenshtein")
expect_identical(tree3$distance_metric(), "hamming")
expect_identical(tree4$distance_metric(), "hamming")
expect_identical(tree5$distance_metric(), "hamming_shift")
expect_identical(tree6$distance_metric(), "hamming_shift")
expect_identical(tree5$maximal_absolute_shift(), 5L)
expect_identical(tree6$maximal_absolute_shift(), 0L)
# add sequences
expect_error(tree$insert(seqs))
expect_identical(tree$size, 0)
expect_identical(tree2$size, 0)
for (s in seqs) {
tree$insert(s)
tree2$insert(s)
}
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
expect_identical(tree3$size, n)
tree$insert(seqs[1])
tree2$insert(seqs[1])
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
# check presence
expect_true(tree$has(seqs[1], 0))
expect_true(tree2$has(seqs[1], 0))
expect_true(tree$has(seqs[1], k))
expect_true(tree2$has(seqs[1], k))
expect_false(tree$has("non_existing", 0))
expect_false(tree2$has("non_existing", 0))
# get first element
expect_identical(tree$first(), seqs[1])
expect_identical(tree2$first(), seqs[1])
# memory size
expect_type(m <- tree$capacity(), "integer")
expect_true(m > 0 && m < n * k * 8)
expect_identical(tree2$capacity(), m)
expect_identical(tree3$remove(seqs[n]), NULL)
expect_type(m3 <- tree3$capacity(), "integer")
expect_true(m3 > 0 && m3 < (n - 1) * k * 8)
expect_identical(tree3$insert(seqs[n]), NULL)
# print tree
expect_output(tree$print(), paste0("^", n, ".+0: ", seqs[1]))
expect_output(tree2$print(), paste0("^", n, ".+0: ", seqs[1]))
expect_identical(tree3$remove(seqs[n]), NULL)
expect_output(tree3$print(), paste0("^", n - 1, ".+0: ", seqs[1]))
expect_identical(tree3$insert(seqs[n]), NULL)
expect_output(tree4$print(), "^0$")
# search similar sequences
# ... hamming distances
# ground truth from: sum(stringdist::stringdist(seqs[1], seqs, method = "hamming") <= 24)
res <- tree$search(seqs[1], 0)
expect_type(res, "character")
expect_length(res, 1L)
expect_length(tree$search(seqs[1], 1), 5L)
expect_length(tree$search(seqs[1], 24), 14L)
expect_length(tree$search(seqs[2], 2), 1L)
expect_length(tree$search(seqs[2], 17), 1L)
expect_length(tree$search(seqs[2], 23), 9L)
expect_length(tree$search(seqs[2], 26), 16L)
expect_length(tree$search(seqs[2], 27), 20L)
expect_length(tree$search(seqs[2], 30), 20L)
expect_true(all(tree$search(seqs[2], 23) %in% seqs))
# ... hamming+shift distances
expect_identical(tree4$size, 0)
expect_identical(tree5$size, 0)
expect_identical(tree6$size, 0)
for (s in c("CGATCGATGCAA", "AACGATCGATGC")) {
tree4$insert(s)
tree5$insert(s)
tree6$insert(s)
}
expect_identical(tree4$size, 2)
expect_identical(tree5$size, 2)
expect_identical(tree6$size, 2)
expect_length(tree4$search("CGATCGATGCAA", 0), 1L)
expect_length(tree4$search("CGATCGATGCAA", 11), 1L)
expect_length(tree4$search("CGATCGATGCAA", 12), 2L)
expect_length(tree5$search("CGATCGATGCAA", 0), 1L)
expect_length(tree5$search("CGATCGATGCAA", 3), 1L)
expect_length(tree5$search("CGATCGATGCAA", 4), 2L)
expect_length(tree6$search("CGATCGATGCAA", 0), 1L)
expect_length(tree6$search("CGATCGATGCAA", 11), 1L)
expect_length(tree6$search("CGATCGATGCAA", 12), 2L)
# ... levenshtein distances
# ground truth from: sum(stringdist::stringdist(seqs[1], seqs, method = "lv") <= 24)
res <- tree2$search(seqs[1], 0)
expect_type(res, "character")
expect_length(res, 1L)
expect_length(tree2$search(seqs[1], 1), 5L)
expect_length(tree2$search(seqs[1], 18), 8L)
expect_length(tree2$search(seqs[2], 2), 1L)
expect_length(tree2$search(seqs[2], 17), 3L)
expect_length(tree2$search(seqs[2], 18), 6L)
expect_length(tree2$search(seqs[2], 19), 13L)
expect_length(tree2$search(seqs[2], 20), 18L)
expect_length(tree2$search(seqs[2], 30), 20L)
expect_true(all(tree2$search(seqs[2], 19) %in% seqs))
# remove sequences
expect_identical(tree$remove("non_existing"), NULL)
expect_identical(tree2$remove("non_existing"), NULL)
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
r <- ceiling(n * 0.7)
for (i in seq_len(r)) {
tree$remove(seqs[i])
tree2$remove(seqs[i])
}
expect_identical(tree$size, n - r)
expect_identical(tree2$size, n - r)
expect_identical(tree$remove_all(), NULL)
expect_identical(tree2$remove_all(), NULL)
expect_identical(tree$size, 0)
expect_identical(tree2$size, 0)
expect_identical(tree3$size, n)
expect_type(tree3$remove(seqs[1]), "NULL")
expect_identical(tree3$size, n - 1)
expect_type(tree3$insert(seqs[1]), "NULL")
expect_identical(tree3$size, n)
# check existing elements
expect_identical(tree$remove_all(), NULL)
expect_identical(tree2$remove_all(), NULL)
expect_identical(tree$search(seqs[1], 0), character(0))
expect_identical(tree2$has(seqs[1], 0), FALSE)
for (s in seqs) {
tree$insert(s)
tree2$insert(s)
}
expect_type(res <- tree$get_all(), "character")
expect_type(res2 <- tree2$get_all(), "character")
expect_identical(seqs, res)
expect_identical(seqs, res2)
set.seed(43)
i <- sample(length(seqs), round(length(seqs) / 3))
for (ii in i) {
tree$remove(seqs[ii])
tree2$remove(seqs[ii])
}
expect_type(res <- tree$get_all(), "character")
expect_type(res2 <- tree2$get_all(), "character")
expect_identical(seqs[-i], res)
expect_identical(seqs[-i], res2)
})
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test_that("levenshtein_distance() works", {
# ground truth e.g. from:
# stringdist::stringdist(s1, s2, method = "lv")
s1 <- "AAAAAAACCC"
s2 <- "AAAAAACCCC"
s3 <- "ACGTACGTACGT"
s4 <- "CGTACGTACGTA"
expect_error(levenshtein_distance(c(s1, s1), s2))
expect_error(levenshtein_distance(s1, c(s2, s2)))
expect_identical(levenshtein_distance(s1, s1), 0L)
expect_identical(levenshtein_distance(s2, s2), 0L)
expect_identical(levenshtein_distance(s3, s3), 0L)
expect_identical(levenshtein_distance(s4, s4), 0L)
expect_identical(levenshtein_distance(s1, s2), 1L)
expect_identical(levenshtein_distance(s1, s3), 8L)
expect_identical(levenshtein_distance(s1, s4), 9L)
expect_identical(levenshtein_distance(s2, s3), 9L)
expect_identical(levenshtein_distance(s2, s4), 9L)
expect_identical(levenshtein_distance(s3, s4), 2L)
})
test_that("hamming_distance() works", {
# ground truth e.g. from:
# stringdist::stringdist(s1, s2, method = "hamming")
s1 <- "AAAAAAACCC"
s2 <- "AAAAAACCCC"
s3 <- "ACGTACGTACGT"
s4 <- "CGTACGTACGTA"
expect_error(hamming_distance(c(s1, s1), s2))
expect_error(hamming_distance(s1, c(s2, s2)))
expect_identical(hamming_distance(s1, s1), 0L)
expect_identical(hamming_distance(s2, s2), 0L)
expect_identical(hamming_distance(s3, s3), 0L)
expect_identical(hamming_distance(s4, s4), 0L)
expect_identical(hamming_distance(s1, s2), 1L)
expect_identical(hamming_distance(s2, s1), 1L)
expect_identical(hamming_distance(s3, s4), 12L)
expect_identical(hamming_distance(s4, s3), 12L)
})
test_that("hamming_shift_distance() works", {
# ground truth e.g. from:
# s <- 1; stringdist::stringdist(substr(s1, 1, 15 - s), substr(s2, 1 + s, 15), "hamming") + 2 * s
# s <- 1; stringdist::stringdist(substr(s2, 1, 15 - s), substr(s1, 1 + s, 15), "hamming") + 2 * s
s1 <- "AAACAAAACGTTGCC"
s2 <- "ACAAAACGTTGCCCC"
s3 <- "AGTCATGCTTAGAAA"
s4 <- "AAAAGTCATGCTTAG"
expect_error(hamming_shift_distance(c(s1, s1), s2))
expect_error(hamming_shift_distance(s1, c(s2, s2)))
expect_error(hamming_shift_distance(s1, s2, c(1L, -1L)))
expect_identical(hamming_shift_distance(s1, s1), 0L)
expect_identical(hamming_shift_distance(s2, s2), 0L)
expect_identical(hamming_shift_distance(s3, s3), 0L)
expect_identical(hamming_shift_distance(s4, s4), 0L)
expect_identical(hamming_shift_distance(s1, s2, 0), 9L)
expect_identical(hamming_shift_distance(s1, s2, 1), 9L)
expect_identical(hamming_shift_distance(s1, s2, 2), 4L)
expect_identical(hamming_shift_distance(s1, s2, 3), 4L)
expect_identical(hamming_shift_distance(s1, s2, -1), 4L)
expect_identical(hamming_shift_distance(s3, s4, 0), 11L)
expect_identical(hamming_shift_distance(s3, s4, 1), 11L)
expect_identical(hamming_shift_distance(s3, s4, 2), 11L)
expect_identical(hamming_shift_distance(s3, s4, 3), 6L)
expect_identical(hamming_shift_distance(s3, s4, -1), 6L)
})
# using Rcpp-module that exposes the BKtree class to R
test_that("low-level BKtree wrapper functions work as expected", {
# create random k-mers
set.seed(42)
k <- 30L
n <- 20
alph <- c("A","C","G","T","N")
seqs <- unlist(lapply(seq_len(n - length(alph) + 1),
function(i) paste(sample(alph, size = k, replace = TRUE),
collapse = "")))
seqs <- c(seqs, paste0(setdiff(alph, substr(seqs[1], 1, 1)),
substr(seqs[1], 2, k)))
# load module and create tree instances
bk <- Rcpp::Module("mod_BKtree", PACKAGE = "mutscan")
BKtree <- bk$BKtree
expect_error(new(BKtree, "error"))
# expect_error(new(BKtree, seqs, "error")) # triggers an unrecoverable crash in BioC 3.17 -> deactivate
expect_error(new(BKtree, seqs, "hamming_shift", c(1L, -1L)))
tree <- new(BKtree)
tree2 <- new(BKtree, "levenshtein")
tree3 <- new(BKtree, seqs[c(seq.int(n), seq.int(n))], "hamming", -1)
tree4 <- new(BKtree, character(0), "hamming", -1)
tree5 <- new(BKtree, "hamming_shift", 5L)
tree6 <- new(BKtree, "hamming_shift", 0L)
expect_s4_class(bk, "Module")
expect_s4_class(BKtree, "C++Class")
expect_s4_class(tree, "Rcpp_BKtree")
expect_s4_class(tree2, "Rcpp_BKtree")
expect_s4_class(tree3, "Rcpp_BKtree")
expect_s4_class(tree4, "Rcpp_BKtree")
expect_s4_class(tree5, "Rcpp_BKtree")
expect_s4_class(tree6, "Rcpp_BKtree")
expect_identical(tree$distance_metric(), "hamming")
expect_identical(tree2$distance_metric(), "levenshtein")
expect_identical(tree3$distance_metric(), "hamming")
expect_identical(tree4$distance_metric(), "hamming")
expect_identical(tree5$distance_metric(), "hamming_shift")
expect_identical(tree6$distance_metric(), "hamming_shift")
expect_identical(tree5$maximal_absolute_shift(), 5L)
expect_identical(tree6$maximal_absolute_shift(), 0L)
# add sequences
expect_error(tree$insert(seqs))
expect_identical(tree$size, 0)
expect_identical(tree2$size, 0)
for (s in seqs) {
tree$insert(s)
tree2$insert(s)
}
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
expect_identical(tree3$size, n)
tree$insert(seqs[1])
tree2$insert(seqs[1])
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
# check presence
expect_true(tree$has(seqs[1], 0))
expect_true(tree2$has(seqs[1], 0))
expect_true(tree$has(seqs[1], k))
expect_true(tree2$has(seqs[1], k))
expect_false(tree$has("non_existing", 0))
expect_false(tree2$has("non_existing", 0))
# get first element
expect_identical(tree$first(), seqs[1])
expect_identical(tree2$first(), seqs[1])
# memory size
expect_type(m <- tree$capacity(), "integer")
expect_true(m > 0 && m < n * k * 8)
expect_identical(tree2$capacity(), m)
expect_identical(tree3$remove(seqs[n]), NULL)
expect_type(m3 <- tree3$capacity(), "integer")
expect_true(m3 > 0 && m3 < (n - 1) * k * 8)
expect_identical(tree3$insert(seqs[n]), NULL)
# print tree
expect_output(tree$print(), paste0("^", n, ".+0: ", seqs[1]))
expect_output(tree2$print(), paste0("^", n, ".+0: ", seqs[1]))
expect_identical(tree3$remove(seqs[n]), NULL)
expect_output(tree3$print(), paste0("^", n - 1, ".+0: ", seqs[1]))
expect_identical(tree3$insert(seqs[n]), NULL)
expect_output(tree4$print(), "^0$")
# search similar sequences
# ... hamming distances
# ground truth from: sum(stringdist::stringdist(seqs[1], seqs, method = "hamming") <= 24)
res <- tree$search(seqs[1], 0)
expect_type(res, "character")
expect_length(res, 1L)
expect_length(tree$search(seqs[1], 1), 5L)
expect_length(tree$search(seqs[1], 24), 14L)
expect_length(tree$search(seqs[2], 2), 1L)
expect_length(tree$search(seqs[2], 17), 1L)
expect_length(tree$search(seqs[2], 23), 9L)
expect_length(tree$search(seqs[2], 26), 16L)
expect_length(tree$search(seqs[2], 27), 20L)
expect_length(tree$search(seqs[2], 30), 20L)
expect_true(all(tree$search(seqs[2], 23) %in% seqs))
# ... hamming+shift distances
expect_identical(tree4$size, 0)
expect_identical(tree5$size, 0)
expect_identical(tree6$size, 0)
for (s in c("CGATCGATGCAA", "AACGATCGATGC")) {
tree4$insert(s)
tree5$insert(s)
tree6$insert(s)
}
expect_identical(tree4$size, 2)
expect_identical(tree5$size, 2)
expect_identical(tree6$size, 2)
expect_length(tree4$search("CGATCGATGCAA", 0), 1L)
expect_length(tree4$search("CGATCGATGCAA", 11), 1L)
expect_length(tree4$search("CGATCGATGCAA", 12), 2L)
expect_length(tree5$search("CGATCGATGCAA", 0), 1L)
expect_length(tree5$search("CGATCGATGCAA", 3), 1L)
expect_length(tree5$search("CGATCGATGCAA", 4), 2L)
expect_length(tree6$search("CGATCGATGCAA", 0), 1L)
expect_length(tree6$search("CGATCGATGCAA", 11), 1L)
expect_length(tree6$search("CGATCGATGCAA", 12), 2L)
# ... levenshtein distances
# ground truth from: sum(stringdist::stringdist(seqs[1], seqs, method = "lv") <= 24)
res <- tree2$search(seqs[1], 0)
expect_type(res, "character")
expect_length(res, 1L)
expect_length(tree2$search(seqs[1], 1), 5L)
expect_length(tree2$search(seqs[1], 18), 8L)
expect_length(tree2$search(seqs[2], 2), 1L)
expect_length(tree2$search(seqs[2], 17), 3L)
expect_length(tree2$search(seqs[2], 18), 6L)
expect_length(tree2$search(seqs[2], 19), 13L)
expect_length(tree2$search(seqs[2], 20), 18L)
expect_length(tree2$search(seqs[2], 30), 20L)
expect_true(all(tree2$search(seqs[2], 19) %in% seqs))
# remove sequences
expect_identical(tree$remove("non_existing"), NULL)
expect_identical(tree2$remove("non_existing"), NULL)
expect_identical(tree$size, n)
expect_identical(tree2$size, n)
r <- ceiling(n * 0.7)
for (i in seq_len(r)) {
tree$remove(seqs[i])
tree2$remove(seqs[i])
}
expect_identical(tree$size, n - r)
expect_identical(tree2$size, n - r)
expect_identical(tree$remove_all(), NULL)
expect_identical(tree2$remove_all(), NULL)
expect_identical(tree$size, 0)
expect_identical(tree2$size, 0)
expect_identical(tree3$size, n)
expect_type(tree3$remove(seqs[1]), "NULL")
expect_identical(tree3$size, n - 1)
expect_type(tree3$insert(seqs[1]), "NULL")
expect_identical(tree3$size, n)
# check existing elements
expect_identical(tree$remove_all(), NULL)
expect_identical(tree2$remove_all(), NULL)
expect_identical(tree$search(seqs[1], 0), character(0))
expect_identical(tree2$has(seqs[1], 0), FALSE)
for (s in seqs) {
tree$insert(s)
tree2$insert(s)
}
expect_type(res <- tree$get_all(), "character")
expect_type(res2 <- tree2$get_all(), "character")
expect_identical(seqs, res)
expect_identical(seqs, res2)
set.seed(43)
i <- sample(length(seqs), round(length(seqs) / 3))
for (ii in i) {
tree$remove(seqs[ii])
tree2$remove(seqs[ii])
}
expect_type(res <- tree$get_all(), "character")
expect_type(res2 <- tree2$get_all(), "character")
expect_identical(seqs[-i], res)
expect_identical(seqs[-i], res2)
})
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