context("MSA")
test_that("read_query_alignment works", {
x <- get_test_query_alignment()
expect_that(x, is_a('AAStringSet'))
expect_that(digest(x), equals("49892fc52f9dc19bbbaf41227450ff20"))
})
test_that("get_patient_ids work", {
x <- get_test_query_alignment()
ids <- get_patient_ids(x)
expect_true("hxb2" %in% ids)
expect_false("hxb2 " %in% ids)
expect_true("pat02" %in% ids)
x <- AAStringSet(structure(c( "MG", "MG", "MG", "MG"),
.Names = c("17h00,hxb2 ,sdklfj",
"45h34,pat01,scribbles",
",pat02",
"hello, pat03")))
ids <- get_patient_ids(x, ',', 2)
expect_true("hxb2" %in% ids)
expect_false("hxb2 " %in% ids)
expect_true("pat02" %in% ids)
expect_false("hello" %in% ids)
ids <- get_patient_ids(x, sep = NULL)
expect_true("17h00,hxb2 ,sdklfj" %in% ids)
})
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