tests/testthat/test_gGnome_utils.R

In mskilab/gGnome: gGnome: reference based assembly graph for analyzing rearranged genomes

library(testthat)
library(gUtils)

setDTthreads(1)

## test_that('read_xmap, read_cmap', {
##     # one test for read_xmap is already included in the haplograph tests
##     # here we only test compliment functions not tested there
##     system('wget https://mskilab.s3.amazonaws.com/gGnome/H838-bionano.tar.gz && tar -xzvf H838-bionano.tar.gz')
##     xmap.fn = './H838-bionano/EXP_REFINEFINAL1.xmap'

##     # test win and grl = FALSE #
##     win = '1:627999-1213255'
##     gr = xmap.fn %>% read_xmap(merge = FALSE, verbose = TRUE, win = win, grl = FALSE)
##     expect_true(gr.string(gr.stripstrand(gr %>% reduce)) == win)

##     # test seqlevels #
##     seqlevels.dict = c(1:22, 'X', 'Y')
##     names(seqlevels.dict) = 1:24
##     gr1 = xmap.fn %>% read_xmap(merge = FALSE, verbose = TRUE, seqlevels = seqlevels.dict)
##     expect_true(all(sort(seqlevels(gr1)) == sort(as.character(seqlevels.dict))))

##     expect_warning(read_cmap('/dev/null'))
##     expect_warning(read_cmap('/dev/null', gr = FALSE))

##     cmap.fn = './H838-bionano/EXP_REFINEFINAL1.cmap'
##     cmap.gr = read_cmap(cmap.fn, gr = TRUE)
##     expect_true(inherits(cmap.gr, 'GRanges'))

##     # test read_xmap with merge and lift
##     gr = xmap.fn %>% read_xmap(merge = TRUE, lift = TRUE, verbose = TRUE, grl = FALSE)

##     expect_warning(read_xmap('/dev/null'))
##     expect_warning(read_xmap('/dev/null', grl = FALSE))

## })

test_that(desc = "test function dt_na2false", code = {
    tst.dt = data.table(a = sample(c(TRUE, FALSE, NA), size = 20, replace = TRUE),
                        b = NA,
                        c = sample(c("a", "b", "c"), size = 20, replace = TRUE))
    dt1 = dt_na2false(tst.dt, these_cols = NULL)
    tst.dt = data.table(a = sample(c(TRUE, FALSE, NA), size = 20, replace = TRUE),
                        b = NA,
                        c = sample(c("a", "b", "c"), size = 20, replace = TRUE))
    dt2 = dt_na2false(tst.dt, these_cols = "a")
    expect_true(all(!is.na(dt1[, a])))
    expect_true(all(!is.na(dt1[, b])))
    expect_true(all(!is.na(dt2[, a])))
    expect_true(all(is.na(dt2[, b])))
})