tests/testthat/test-methods.R

In MahShaaban/Rfastqc: Read FastQC output

library(dplyr)
context("methods")

test_that('test_get', {
    fl <- system.file("extdata", "sample_1.txt", package = "Rfastqc")
    fqc <- parse_fqc(fl)
    fqc <- FastQC(fqc)

    expect_error(test_get(fqc))

    tst_dat <- test_get(fqc, test = 'Per base sequence quality')

    expect_true(is.factor(tst_dat$Base))
    expect_true(all(apply(tst_dat[, -1], 2, is.numeric)))
})

test_that('plot.FastQC', {
    fl <- system.file("extdata", "sample_1.txt", package = "Rfastqc")
    fqc <- parse_fqc(fl)
    fqc <- FastQC(fqc)
    nms <- names(fqc)
    expect_error(plot(fqc), 'User Should provied a test name.')
    expect_error(plot(fqc, test = nms[1]),
               'Nothing to plot. Use test_get instead.')
    expect_error(plot(fqc, test = nms[10]),
               'Nothing to plot. Use summary instead.')
    expect_silent(plot(fqc, test = nms[2]))
})

test_that('plot.multiFastQC', {
    path <- system.file('extdata', package = 'Rfastqc')
    fls <- list.files(path, pattern = '*.txt', full.names = TRUE)
    fqc <- parse_collection(fls)
    fqc <- multiFastQC(fqc)
    nms <- names(fqc)
    expect_error(plot(fqc), 'User should provide a test name.')
    expect_silent(plot(fqc, test = nms[2]))
})


# clean
unlink('*.pdf')