def test_run_with_pvalue_exceeded(self):
temp_dir = tempfile.mkdtemp()
try:
enrichr = MagicMock()
df = pd.DataFrame(columns=[
'Term', 'Gene_set', 'P-value', 'Adjusted P-value', 'Genes',
'Overlap'
],
data=[['term1', 'set1', 1.5, 0.6, 'B;C', '2/25'],
['term2', 'set2', 1.6, 0.7, 'A;C', '7/9']])
txt_file = os.path.join(temp_dir, 'data.txt')
df.to_csv(txt_file, index=False, sep='\t', encoding='utf-8')
enrichr.enrichr = MagicMock(return_value=enrichr)
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c')
myargs = [tfile, '--tmpdir', temp_dir]
theargs = cdenrichrgenestoterm._parse_arguments('desc', myargs)
res = cdenrichrgenestoterm.run_enrichr(tfile,
theargs,
enrichr=enrichr)
gs = self.get_default_genesets()
self.assertEqual(None, res)
enrichr.enrichr.assert_called_once_with(gene_list=['A', 'B', 'C'],
cutoff=0.05,
gene_sets=gs,
no_plot=True,
outdir=temp_dir)
finally:
shutil.rmtree(temp_dir)
def test_run_where_enrichr_raises_exception(self):
temp_dir = tempfile.mkdtemp()
try:
enrichr = MagicMock()
enrichr.enrichr = MagicMock()
enrichr.enrichr.side_effect = Exception('Some exception')
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c')
myargs = [tfile, '--tmpdir', temp_dir]
theargs = cdenrichrgenestoterm._parse_arguments('desc', myargs)
res = cdenrichrgenestoterm.run_enrichr(tfile,
theargs,
enrichr=enrichr)
gs = self.get_default_genesets()
self.assertEqual(None, res)
the_call = call(gene_list=['A', 'B', 'C'],
cutoff=0.05,
gene_sets=gs,
no_plot=True,
outdir=temp_dir)
enrichr.enrichr.assert_has_calls([the_call, the_call])
finally:
shutil.rmtree(temp_dir)
def test_parse_args(self):
myargs = ['inputarg']
res = cdenrichrgenestoterm._parse_arguments('desc', myargs)
self.assertEqual('inputarg', res.input)
self.assertEqual(0.05, res.maxpval)
self.assertEqual('/tmp', res.tmpdir)
self.assertEqual(
'GO_Biological_Process_2018,' + 'GO_Cellular_Component_2018,' +
'GO_Molecular_Function_2018', res.genesets)
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 = cdenrichrgenestoterm._parse_arguments('desc', myargs)
res = cdenrichrgenestoterm.run_enrichr(tfile, theargs)
self.assertEqual(None, res)
finally:
shutil.rmtree(temp_dir)
def test_run_with_valid_result_from_multiple_genesets(self):
temp_dir = tempfile.mkdtemp()
try:
enrichr = MagicMock()
df = pd.DataFrame(
columns=[
'Term', 'Gene_set', 'P-value', 'Adjusted P-value', 'Genes',
'Overlap'
],
data=[['term1', 'set1', 0.6, 0.05, 'B;C', '2/25'],
['term2', 'set2', 0.5, 0.03, 'A;C', '7/9']])
txt_file = os.path.join(temp_dir, 'data.txt')
df.to_csv(txt_file, index=False, sep='\t', encoding='utf-8')
df = pd.DataFrame(
columns=[
'Term', 'Gene_set', 'P-value', 'Adjusted P-value', 'Genes',
'Overlap'
],
data=[['term5', 'set1', 0.6, 0.01, 'B;C', '2/25'],
['term6', 'set2', 0.5, 0.03, 'X;Y', '7/8']])
txt_file = os.path.join(temp_dir, 'data2.txt')
df.to_csv(txt_file, index=False, sep='\t', encoding='utf-8')
# make a directory with .txt ending just for fun
os.makedirs(os.path.join(temp_dir, 'haha.txt'), mode=0o755)
enrichr.enrichr = MagicMock(return_value=enrichr)
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c')
myargs = [tfile, '--tmpdir', temp_dir]
theargs = cdenrichrgenestoterm._parse_arguments('desc', myargs)
res = cdenrichrgenestoterm.run_enrichr(tfile,
theargs,
enrichr=enrichr)
gs = self.get_default_genesets()
self.assertEqual('term5', res['name'])
self.assertEqual('set1', res['source'])
self.assertEqual(0.01, res['p_value'])
self.assertEqual('', res['description'])
self.assertEqual(['B', 'C'], res['intersections'])
self.assertEqual(25, res['term_size'])
enrichr.enrichr.assert_called_once_with(gene_list=['A', 'B', 'C'],
cutoff=0.05,
gene_sets=gs,
no_plot=True,
outdir=temp_dir)
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 = cdenrichrgenestoterm._parse_arguments('desc', myargs)
try:
cdenrichrgenestoterm.run_enrichr(tfile, theargs)
self.fail('Expected FileNotFoundError')
except FileNotFoundError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_with_empty_result(self):
temp_dir = tempfile.mkdtemp()
try:
enrichr = MagicMock()
enrichr.enrichr = MagicMock(return_value=enrichr)
tfile = os.path.join(temp_dir, 'foo')
with open(tfile, 'w') as f:
f.write('a,b,c')
myargs = [tfile, '--tmpdir', temp_dir]
theargs = cdenrichrgenestoterm._parse_arguments('desc', myargs)
res = cdenrichrgenestoterm.run_enrichr(tfile,
theargs,
enrichr=enrichr)
gs = self.get_default_genesets()
self.assertEqual(None, res)
enrichr.enrichr.assert_called_once_with(gene_list=['A', 'B', 'C'],
cutoff=0.05,
gene_sets=gs,
no_plot=True,
outdir=temp_dir)
finally:
shutil.rmtree(temp_dir)