class TestGenePanelCreator(unittest.TestCase):
def setUp(self):
self.ens_ids = 'data/ens_ids.txt'
self.gene_names = 'data/gene_names.txt'
self.idx_file = 'data/Homo_sapiens.GRCh37.75.gtf.gz.index'
self.log = 'data/test_log.log'
self.ens_out = 'data/ens_out.bed'
self.gene_out = 'data/gene_out.bed'
self.gpc = GenePanelCreator(self.idx_file, out_file=self.ens_out, log_file=self.log,
padding='20,10', upstream=200, downstream=200)
def tearDown(self):
for i in [self.ens_out, self.gene_out, self.log]:
if os.path.exists(i):
os.remove(i)
@unittest.skipIf(True, "Lebo")
def test_prepare_genes_with_ensids(self):
ens = self.gpc.prepare_genes(self.ens_ids)
self.assertTrue(len(ens) == 2)
self.assertEqual(ens[0].gene_id, 'ENSG00000006071')
self.assertTrue('HNF4A' in ens[1].names)
@unittest.skipIf(True, "Lebo")
def test_prepare_genes_with_assocnames(self):
ang = self.gpc.prepare_genes(self.gene_names)
def setUp(self):
self.ens_ids = 'data/ens_ids.txt'
self.gene_names = 'data/gene_names.txt'
self.idx_file = 'data/Homo_sapiens.GRCh37.75.gtf.gz.index'
self.log = 'data/test_log.log'
self.ens_out = 'data/ens_out.bed'
self.gene_out = 'data/gene_out.bed'
self.gpc = GenePanelCreator(self.idx_file, out_file=self.ens_out, log_file=self.log,
padding='20,10', upstream=200, downstream=200)