def test_analysis(krakendb):
file1 = sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")
file2 = sequana_data("Hm2_GTGAAA_L005_R2_001.fastq.gz")
# Test that database must be provided
try:
df = taxonomy.main([prog, '--file1', file1])
assert False
except:
assert True
from tempfile import TemporaryDirectory
directory = TemporaryDirectory()
# If on travis and we could not load the database, use the local one
# that must have been downloaded
try:
df = taxonomy.main([
prog, '--file1', file1, "--database", "toydb", "--file2", file2,
"--level", "INFO", "--output-directory", directory.name,
"--thread", "1"
])
except:
# For travis test
HOME = os.getenv('HOME')
database = os.sep.join([HOME, '.config', 'sequana', 'kraken_toydb'])
df = taxonomy.main([
prog, '--file1', file1, "--database", database, "--file2", file2,
"--output-directory", directory.name, "--thread", "1"
])
from sequana import logger
logger.info(directory.name)
def test_help():
try:
taxonomy.main([prog, '--help', '1>/tmp/out', '2>/tmp/err'])
assert False
except SystemExit:
pass
else:
raise Exception
def krakendb():
# todo
try:
taxonomy.main([prog, '--download', 'toydb'])
except TypeError: # Fails on travis so we download manually (appdirs returns
# none instead of the expected user config path
HOME = os.getenv('HOME')
from sequana.misc import wget
baseurl = "https://github.com/sequana/data/raw/master/kraken_toydb/"
filenames = [
"database.idx", "database.kdb", "taxonomy/names.dmp",
"taxonomy/nodes.dmp"
]
for filename in filenames:
from easydev import mkdirs
mkdirs(HOME + os.sep + "database/taxonomy")
wget(baseurl + os.sep + filename,
os.sep.join([HOME, "database", filename]))
except SystemExit:
pass
def test_wrong_db():
try:
df = taxonomy.main([prog, "--database", "dummy"])
assert False
except:
assert True