tests/testthat/test_03_read_profile.R

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

library("seqCAT")
context("Read SNV profiles")

# Paths
file_1 <- system.file("extdata", "test_1.profile.txt.gz", package = "seqCAT")
file_2 <- system.file("extdata", "test_2.profile.txt.gz", package = "seqCAT")
file_3 <- system.file("extdata", "test_3.profile.txt.gz", package = "seqCAT")
file_bed <- system.file("extdata", "test_1.profile.bed.gz", package = "seqCAT")
file_gtf <- system.file("extdata", "test_1.profile.gtf.gz", package = "seqCAT")
file_gff <- system.file("extdata", "test_1.profile.gff.gz", package = "seqCAT")
profile_dir <- system.file("extdata", package = "seqCAT")

# Read profiles
test_1 <- suppressMessages(read_profile(file = file_1))
test_2 <- suppressMessages(read_profile(file = file_2))
test_3 <- suppressMessages(read_profile(file = file_3))
test_bed <- suppressMessages(read_profile(file = file_bed))
test_gtf <- suppressMessages(read_profile(file = file_gtf))
test_gff <- suppressMessages(read_profile(file = file_gff))
test_dir <- suppressMessages(read_profiles(profile_dir = profile_dir))
test_name <- suppressMessages(read_profile(file = file_1,
                                           sample_name = "new_name"))

# Tests
test_that("correct object types are returned", {
    expect_identical(class(test_1)[1], "data.frame")
    expect_identical(class(test_bed)[1], "data.frame")
    expect_identical(class(test_gtf)[1], "data.frame")
    expect_identical(class(test_gff)[1], "data.frame")
    expect_identical(class(test_dir)[1], "list")
})

test_that("correct number of variants are read", {
    expect_equal(dim(test_1), c(377, 19))
    expect_equal(dim(test_2), c(375, 19))
    expect_equal(dim(test_bed), c(377, 2))
    expect_equal(dim(test_gtf), c(377, 19))
    expect_equal(dim(test_gff), c(377, 2))
    expect_equal(dim(test_dir[[1]]), c(377, 19))
})

test_that("profiles without variant annotations are handled correctly", {
    expect_equal(nrow(test_3), 99)
})

test_that("unsupported format specifications are handled correctly", {
    expect_error(read_profile("test.bef"),
                 "Unsupported format specification \"")
})

test_that("sample names can be overridden correctly", {
    expect_identical(unique(test_name$sample), "new_name")
})