# LIBS
library(testthat)
# VARS
data_d <- testdatadir_get()
# DATA
# TODO: get ten random records of each NCBI domain
records <- readRDS(file = file.path(data_d, 'records.RData'))
# RUNNING
context('Testing \'extract-tools\'')
test_that('extract_by_patterns() works', {
record <- sample(records, 1)[[1]]
res <- extract_by_patterns(record = record,
start_pattern = '\nFEATURES\\s{2,}')
expect_true(grepl('Location/Qualifiers', res))
})
test_that('extract_version() works', {
record <- sample(records, 1)[[1]]
accession_version <- extract_version(record = record)
# print(accession_version)
expect_true(grepl('^[a-z0-9_]+\\.[0-9]+$', accession_version,
ignore.case = TRUE))
})
test_that('extract_organism() works', {
record <- sample(records, 1)[[1]]
organism <- extract_organism(record = record)
# print(organism)
expect_false(grepl('\\s{2,}', organism,
ignore.case = TRUE))
expect_false(grepl('\n', organism, ignore.case = TRUE))
})
test_that('extract_definition() works', {
record <- sample(records, 1)[[1]]
definition <- extract_definition(record = record)
#print(definition)
expect_false(grepl('\\s{2,}', definition,
ignore.case = TRUE))
expect_false(grepl('\n', definition, ignore.case = TRUE))
})
test_that('extract_sequence() works', {
record <- sample(records, 1)[[1]]
sequence <- extract_sequence(record = record)
expect_false(grepl('[0-9]', sequence,
ignore.case = TRUE))
})
test_that('extract_features() works', {
record <- sample(records, 1)[[1]]
features <- extract_features(record = record)
# print(features)
expect_true(inherits(features, 'list'))
})
test_that('extract_locus() works', {
record <- sample(records, 1)[[1]]
locus <- extract_locus(record = record)
# print(locus)
expect_true(inherits(locus, 'character'))
})
test_that('extract_keywords() works', {
record <- sample(records, 1)[[1]]
keywords <- extract_keywords(record = record)
# print(keywords)
expect_true(inherits(keywords, 'character'))
})
test_that('gb_extract() works', {
opts <- c('accession', 'version', 'organism','sequence', 'definition',
'locus', 'features', 'keywords')
what <- sample(opts, 1)
record <- sample(records, 1)[[1]]
res <- gb_extract(record = record, what = what)
if (what == 'features') {
expect_true(inherits(res, 'list'))
} else {
expect_true(inherits(res, 'character'))
}
})
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