context("Miscellaneous issues")
test_that("header and data can use different delimiters", {
file <- "tables/different-header-delimiter.txt"
expect_silent(table <- read_gwas(file, verbose = FALSE))
})
test_that("handles compressed files", {
ref <- read_gwas("tables/columns-variant1-canonical.txt")
expect_equal(read_gwas("tables/columns-variant1-canonical.txt.zip"), ref)
expect_equal(read_gwas("tables/columns-variant1-canonical.txt.gz"), ref)
})
test_that("handles multiple files", {
files <- dir("tables", pattern = "variant[234]", full.names = TRUE)
expect_true(is.data.frame(read_gwas(files, chromosome_style = NULL)))
# respects custom names
names(files) <- c("gwas1", "gwas2", "gwas3")
gwas <- read_gwas(files, chromosome_style = NULL)
expect_equal(unique(gwas$.gwas), names(files))
})
test_that("handles column names from pretty printed files", {
gwas <- read_gwas("tables/plink-dosage.txt")
expect_equal(dim(gwas), c(6, 8))
})
test_that("preprocessor can handle ascii null characters", {
file <- "tables/plink-dosage-with-ascii-null.txt"
gwas <- read_gwas(file)
expect_equal(dim(gwas), c(6, 8))
})
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