testthat::test_that("detect_mhc", {
# load test data
alleles <- data.table::rbindlist(
list(
system.file("extdata",
"netMHC_alleles.txt",
package = "antigen.garnish"
) %>%
data.table::fread(header = FALSE, sep = "\t") %>%
data.table::setnames("V1", "allele") %>%
.[, type := "netMHC"],
system.file("extdata",
"netMHCpan_alleles.txt",
package = "antigen.garnish"
) %>%
data.table::fread(header = FALSE, sep = "\t") %>%
data.table::setnames("V1", "allele") %>%
.[, type := "netMHCpan"],
system.file("extdata",
"mhcflurry_alleles.txt",
package = "antigen.garnish"
) %>%
data.table::fread(header = FALSE, sep = "\t") %>%
data.table::setnames("V1", "allele") %>%
.[, type := "mhcflurry"],
system.file("extdata",
"netMHCII_alleles.txt",
package = "antigen.garnish"
) %>%
data.table::fread(header = FALSE, sep = "\t") %>%
data.table::setnames("V1", "allele") %>%
.[, type := "netMHCII"],
system.file("extdata",
"netMHCIIpan_alleles.txt",
package = "antigen.garnish"
) %>%
data.table::fread(header = FALSE, sep = "\t") %>%
data.table::setnames("V1", "allele") %>%
.[, type := "netMHCIIpan"]
)
)
dt <- data.table::data.table(
netMHCIIpan =
c("A0201", "A0301", "DRB1_0301", "DRB1_1467")
)
# run test
dt[, netMHCIIpan := antigen.garnish:::detect_mhc(netMHCIIpan, alleles)]$netMHCIIpan %>%
testthat::expect_equal(c(NA, NA, "DRB1_0301", "DRB1_1467"))
})
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