tests/testthat/test-get_quant_meta.R

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

test_that("get_quant_meta pairs paired GEO fastq.gz files", {
    srp_meta <- data.frame(
        run = "SRR1",
        gsm_name = "GSM4875733",
        library_layout = "PAIRED"
    )

    # example paired fastq files
    data_dir <- tempdir()
    file.create(file.path(data_dir, c("SRR1_1.fastq.gz", "SRR1_2.fastq.gz")))
    quant_meta <- get_quant_meta(srp_meta, data_dir)

    expect_equal(quant_meta$Pair, c(1, 1))
})

test_that("get_quant_meta doesn't pair single-end GEO fastq.gz files", {
    srp_meta <- data.frame(
        run = "SRR1",
        gsm_name = "GSM4875733",
        library_layout = "SINGLE"
    )

    # example paired fastq files
    data_dir <- tempdir()
    file.create(file.path(data_dir, c("SRR1_1.fastq.gz", "SRR1_2.fastq.gz")))
    quant_meta <- get_quant_meta(srp_meta, data_dir)

    expect_equal(quant_meta$Pair, c(NA, NA))
    unlink(list.files(data_dir, '^SRR1_\\d.fastq.gz', full.names = TRUE))
})

test_that("get_quant_meta detects single-ended fastq.gz file", {
    srp_meta <- data.frame(
        run = "SRR1",
        gsm_name = "GSM4875733",
        library_layout = "SINGLE"
    )

    # example paired fastq files
    data_dir <- tempdir()
    file.create(file.path(data_dir, "SRR12323_1.fastq.gz"))
    file.create(file.path(data_dir, "SRR1.fastq.gz"))
    quant_meta <- get_quant_meta(srp_meta, data_dir)

    expect_equal(quant_meta$`File Name`, 'SRR1.fastq.gz')
    unlink(file.path(data_dir, 'SRR1.fastq.gz'))
})