Nothing
library(ptm)
context("Evo traces")
## ---------------------------------------------- ##
# Testing msa #
## ---------------------------------------------- ##
test_that("msa() works properly", {
skip_on_cran()
skip_on_travis()
sequences <- c("MQPIPDVNQRIARISAHLHPPKSQMEESSALRRANCRAKGGAPGFKV",
"MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMM",
"MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMM")
names(sequences) <- c("P19446", "P40925", "P40926")
a <- msa(sequences = sequences, ids = c("wmelon", "cyt", "mit"))
b <- msa(sequences = sequences,
ids = c("wmelon", "cyt", "mit"), inhouse = TRUE)
expect_is(a, "list")
expect_equal(length(a), 4)
expect_is(a[[1]], 'character')
expect_equal(length(a[[1]]), 3)
expect_equal(names(a[[1]]), c("P19446", "P40925", "P40926"))
expect_equivalent(nchar(a[[1]][1]), 47)
expect_is(a[[2]], 'character')
expect_equal(length(a[[2]]), 3)
expect_equal(a[[2]], c("wmelon", "cyt", "mit" ))
expect_equal(length(a[[3]]), 3)
expect_equivalent(nchar(a[[3]][1]), 57)
expect_is(a[[4]], 'matrix')
expect_equal(dim(a[[4]]), c(3, 57))
expect_is(b, "fasta")
expect_equal(length(b), 4)
expect_is(b[[1]], 'character')
expect_equal(length(b[[1]]), 3)
expect_equal(dim(b$ali), c(3,57))
expect_equal(b$id, c("wmelon", "cyt", "mit" ))
})
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