def test_run_gprofiler_with_empty_result(self):
temp_dir = tempfile.mkdtemp()
try:
mygprofiler = MagicMock()
df = pd.DataFrame()
mygprofiler.profile = MagicMock(return_value=df)
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c,')
myargs = [tfile]
theargs = cdgprofilergenestotermcmd._parse_arguments(
'desc', myargs)
res = cdgprofilergenestotermcmd.run_gprofiler(
tfile, theargs, gprofwrapper=mygprofiler)
self.assertEqual(None, res)
mygprofiler.profile.assert_called_once_with(
query=['a', 'b', 'c'],
domain_scope='known',
organism='hsapiens',
user_threshold=0.00000001,
no_evidences=False)
finally:
shutil.rmtree(temp_dir)
def test_parse_args(self):
myargs = ['inputarg']
res = cdgprofilergenestotermcmd._parse_arguments('desc', myargs)
self.assertEqual('inputarg', res.input)
self.assertEqual(0.00000001, res.maxpval)
self.assertEqual(0.05, res.minoverlap)
self.assertEqual('hsapiens', res.organism)
self.assertEqual(500, res.maxgenelistsize)
def test_run_gprofiler_empty_file(self):
temp_dir = tempfile.mkdtemp()
try:
tfile = os.path.join(temp_dir, 'foo')
open(tfile, 'a').close()
myargs = [tfile]
theargs = cdgprofilergenestotermcmd._parse_arguments(
'desc', myargs)
res = cdgprofilergenestotermcmd.run_gprofiler(tfile, theargs)
self.assertEqual(None, res)
finally:
shutil.rmtree(temp_dir)
def test_run_gprofiler_no_file(self):
temp_dir = tempfile.mkdtemp()
try:
tfile = os.path.join(temp_dir, 'foo')
myargs = [tfile]
theargs = cdgprofilergenestotermcmd._parse_arguments(
'desc', myargs)
try:
cdgprofilergenestotermcmd.run_gprofiler(tfile, theargs)
self.fail('Expected FileNotFoundError')
except FileNotFoundError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_gprofiler_with_too_many_genes(self):
temp_dir = tempfile.mkdtemp()
try:
tfile = os.path.join(temp_dir, 'foo')
# write out gene file with 5002 genes which
# should return None
with open(tfile, 'w') as f:
for x in range(0, 5001):
f.write(str(x) + ',')
myargs = [tfile]
theargs = cdgprofilergenestotermcmd._parse_arguments(
'desc', myargs)
res = cdgprofilergenestotermcmd.run_gprofiler(tfile, theargs)
self.assertEqual(None, res)
finally:
shutil.rmtree(temp_dir)
def test_run_gprofiler_with_valid_no_intersections_in_result(self):
temp_dir = tempfile.mkdtemp()
try:
mygprofiler = MagicMock()
df = pd.DataFrame(columns=[
'name', 'source', 'native', 'p_value', 'description',
'intersections', 'precision', 'recall', 'term_size'
],
data=[[
'name1', 'source1', 'native1', 0.1, 'desc1',
['hi'], 0.5, 0.7, 88
],
[
'name2', 'source2', 'native2', 0.5,
'desc2', ['bye'], 0.6, 0.8, 99
]])
mygprofiler.profile = MagicMock(return_value=df)
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c,')
myargs = [tfile]
theargs = cdgprofilergenestotermcmd._parse_arguments(
'desc', myargs)
theargs.omit_intersections = True
res = cdgprofilergenestotermcmd.run_gprofiler(
tfile, theargs, gprofwrapper=mygprofiler)
self.assertEqual('name2', res['name'])
self.assertEqual([], res['intersections'])
self.assertEqual(99, res['term_size'])
self.assertEqual(0.5, res['p_value'])
self.assertEqual('source2', res['source'])
self.assertEqual('native2', res['sourceTermId'])
self.assertEqual(0.522, res['jaccard'])
mygprofiler.profile.assert_called_once_with(
query=['a', 'b', 'c'],
domain_scope='known',
organism='hsapiens',
user_threshold=0.00000001,
no_evidences=True)
finally:
shutil.rmtree(temp_dir)