def test_missing_network_file():
project_name = 'test_missing_network_file'
gene_list = os.path.join(TEST_RESOURCES, 'hgnc_symbols.txt')
args = ArgparseMock(project_name,
gene_list,
'hgnc_symbol',
network_source='sif')
place_resource_files()
run_main(args)
def test_default():
project_name = 'test1'
gene_list = os.path.join(HERE, 'resources', 'hgnc_symbols.txt')
args = ArgparseMock(project_name, gene_list, 'hgnc_symbol')
_place_files()
run_main(args)
assert os.path.exists(TEST_BASE_FOLDER)
assert os.path.exists(
os.path.join(TEST_BASE_FOLDER, project_name, 'genewalk_results.csv'))
def test_default():
project_name = 'test1'
gene_list = os.path.join(TEST_RESOURCES, 'hgnc_symbols.txt')
args = ArgparseMock(project_name, gene_list, 'hgnc_symbol')
place_resource_files()
run_main(args)
assert os.path.exists(TEST_BASE_FOLDER)
result_csv = os.path.join(TEST_BASE_FOLDER, project_name,
'genewalk_results.csv')
assert os.path.exists(result_csv)
df = pandas.read_csv(result_csv)
assert 'MAP2K2' in set(df['hgnc_symbol']), df['hgnc_symbol']
def test_edge_list():
project_name = 'test_edge_list'
gene_list = os.path.join(TEST_RESOURCES, 'hgnc_symbols.txt')
el = os.path.join(TEST_RESOURCES, 'test_edge_list.txt')
args = ArgparseMock(project_name,
gene_list,
'hgnc_symbol',
network_source='edge_list',
network_file=el)
place_resource_files()
run_main(args)
assert os.path.exists(TEST_BASE_FOLDER)
result_csv = os.path.join(TEST_BASE_FOLDER, project_name,
'genewalk_results.csv')
assert os.path.exists(result_csv)
df = pandas.read_csv(result_csv)
assert 'MAP2K2' in set(df['hgnc_symbol']), df['hgnc_symbol']
assert 'GO:0005515' in set(df['go_id'])
assert 'GO:0001934' in set(df['go_id'])
assert 'biological process' in set(df['go_domain'])
def test_custom_genes():
project_name = 'test_custom_genes'
gene_list = os.path.join(TEST_RESOURCES, 'custom_gene_list.txt')
sif = os.path.join(TEST_RESOURCES, 'test_sif_custom.sif')
args = ArgparseMock(project_name,
gene_list,
'custom',
network_source='sif_annot',
network_file=sif)
place_resource_files()
run_main(args)
assert os.path.exists(TEST_BASE_FOLDER)
result_csv = os.path.join(TEST_BASE_FOLDER, project_name,
'genewalk_results.csv')
assert os.path.exists(result_csv)
df = pandas.read_csv(result_csv)
assert 'CUSTOM:ABC' in set(df['custom']), df['custom']
assert 'GO:0000186' in set(df['go_id'])
# In this case we don't have this annotation in the SIF file
assert 'GO:0001934' not in set(df['go_id'])
assert 'biological process' in set(df['go_domain'])
def test_sif_full():
project_name = 'test_sif'
gene_list = os.path.join(TEST_RESOURCES, 'hgnc_symbols.txt')
sif = os.path.join(TEST_RESOURCES, 'test_sif_full.sif')
args = ArgparseMock(project_name,
gene_list,
'hgnc_symbol',
network_source='sif_full',
network_file=sif)
place_resource_files()
run_main(args)
assert os.path.exists(TEST_BASE_FOLDER)
result_csv = os.path.join(TEST_BASE_FOLDER, project_name,
'genewalk_results.csv')
assert os.path.exists(result_csv)
df = pandas.read_csv(result_csv)
assert 'MAP2K2' in set(df['hgnc_symbol']), df['hgnc_symbol']
assert 'GO:0005515' in set(df['go_id'])
# In this case we don't have this annotation in the SIF file
assert 'GO:0001934' not in set(df['go_id'])
# It's particularly important here that we have e.g., GO domains
# since this means that node attributes are added correctly for
# GO terms mentioned in the SIF file
assert 'biological process' in set(df['go_domain'])