Nothing
# LIBS
library(testthat)
# VARS
blast_res_dir <- phylotaR:::datadir_get(file.path('blast', 'blast_res.rda'))
blast_res <- readRDS(file = blast_res_dir)
ps <- parameters()
ps[['wd']] <- phylotaR:::datadir_get('')
# RUNNING
context('Testing \'blast-tools\'')
test_that('blastdb_gen() works', {
sqs <- phylotaR:::testsqs_gen(n = 100)
res <- with_mock(
`phylotaR:::cmdln` = function(...) 0,
phylotaR:::blastdb_gen(sqs = sqs, dbfl = 'testdb', ps = ps)
)
expect_null(res)
res <- with_mock(
`phylotaR:::cmdln` = function(...) 1,
expect_error(phylotaR:::blastdb_gen(sqs = sqs, dbfl = 'testdb', ps = ps))
)
})
test_that('blastn_run() works', {
res <- with_mock(
`phylotaR:::cmdln` = function(...) 0,
phylotaR:::blastn_run(dbfl = 'testdb', outfl = 'testblstn', ps = ps)
)
nms <- colnames(res)
expect_true(all(nms %in% names(blast_res)))
})
test_that('blast_filter() works', {
blast_res <- blast_res[-1, ]
rnd <- sample(2:nrow(blast_res), 2)
blast_res[rnd, 'qcovs'] <- 48
res <- phylotaR:::blast_filter(blast_res = blast_res, ps = ps)
expect_true(nrow(res) < nrow(blast_res))
# make sure rnd and its sq/qs pair is not present
frst <- blast_res[rnd[1], 'query.id'] == res[['query.id']] &
blast_res[rnd[1], 'subject.id'] == res[['subject.id']]
expect_false(any(frst))
scnd <- blast_res[rnd[1], 'subject.id'] == res[['query.id']] &
blast_res[rnd[1], 'query.id'] == res[['subject.id']]
expect_false(any(scnd))
})
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