class TestOrthologClusterer(unittest.TestCase):
def setUp(self):
self._ortholog_clusterer = OrthologClusterer()
def test_process_pairs_to_clusters_3_gene_in_cluster(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[(("gene_A1", "org_A"), ("gene_B1", "org_B")),
(("gene_A1", "org_A"), ("gene_C1", "org_C"))])
orthologs_and_clusters = self._ortholog_clusterer._orthologs_and_clusters
# There must be three orthologs
self.assertEqual(sorted(
orthologs_and_clusters.keys()),
['gene_A1_org_A', 'gene_B1_org_B', 'gene_C1_org_C'])
# All 3 othologos must refer to the same cluster
self.assertEqual(orthologs_and_clusters['gene_A1_org_A'],
orthologs_and_clusters['gene_B1_org_B'])
self.assertEqual(orthologs_and_clusters['gene_A1_org_A'],
orthologs_and_clusters['gene_C1_org_C'])
# The set must contain 3 orthologs
self.assertEqual(len(orthologs_and_clusters['gene_A1_org_A']), 3)
def test_process_pairs_to_clusters_2_gene_in_cluster_1_lonely_gene(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[(("gene_A1", "org_A"), ("gene_B1", "org_B")),
(("gene_C1", "org_C"), None)])
orthologs_and_clusters = self._ortholog_clusterer._orthologs_and_clusters
# There must be three orthologs
self.assertEqual(
sorted(orthologs_and_clusters.keys()),
['gene_A1_org_A', 'gene_B1_org_B', 'gene_C1_org_C'])
# A and B must refer to the same cluster
self.assertEqual(orthologs_and_clusters['gene_A1_org_A'],
orthologs_and_clusters['gene_B1_org_B'])
# C must refer to a cluster of the size 1
self.assertEqual(len(orthologs_and_clusters[
'gene_C1_org_C']), 1)
def test_clusters(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[(("gene_A1", "org_A"), ("gene_B1", "org_B")),
(("gene_A1", "org_A"), ("gene_C1", "org_C")),
(("gene_D1", "org_D"), ("gene_E1", "org_E"))])
clusters = list(self._ortholog_clusterer.clusters())
assert len(clusters) == 2
class TestOrthologClusterer(unittest.TestCase):
def setUp(self):
self._ortholog_clusterer = OrthologClusterer()
def test_process_pairs_to_clusters_3_gene_in_cluster(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[(("gene_A1", "org_A"), ("gene_B1", "org_B")), (("gene_A1", "org_A"), ("gene_C1", "org_C"))]
)
orthologs_and_clusters = self._ortholog_clusterer._orthologs_and_clusters
# There must be three orthologs
self.assertEqual(sorted(orthologs_and_clusters.keys()), ["gene_A1_org_A", "gene_B1_org_B", "gene_C1_org_C"])
# All 3 othologos must refer to the same cluster
self.assertEqual(orthologs_and_clusters["gene_A1_org_A"], orthologs_and_clusters["gene_B1_org_B"])
self.assertEqual(orthologs_and_clusters["gene_A1_org_A"], orthologs_and_clusters["gene_C1_org_C"])
# The set must contain 3 orthologs
self.assertEqual(len(orthologs_and_clusters["gene_A1_org_A"]), 3)
def test_process_pairs_to_clusters_2_gene_in_cluster_1_lonely_gene(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[(("gene_A1", "org_A"), ("gene_B1", "org_B")), (("gene_C1", "org_C"), None)]
)
orthologs_and_clusters = self._ortholog_clusterer._orthologs_and_clusters
# There must be three orthologs
self.assertEqual(sorted(orthologs_and_clusters.keys()), ["gene_A1_org_A", "gene_B1_org_B", "gene_C1_org_C"])
# A and B must refer to the same cluster
self.assertEqual(orthologs_and_clusters["gene_A1_org_A"], orthologs_and_clusters["gene_B1_org_B"])
# C must refer to a cluster of the size 1
self.assertEqual(len(orthologs_and_clusters["gene_C1_org_C"]), 1)
def test_clusters(self):
self._ortholog_clusterer.process_pairs_to_clusters(
[
(("gene_A1", "org_A"), ("gene_B1", "org_B")),
(("gene_A1", "org_A"), ("gene_C1", "org_C")),
(("gene_D1", "org_D"), ("gene_E1", "org_E")),
]
)
clusters = list(self._ortholog_clusterer.clusters())
assert len(clusters) == 2
def setUp(self):
self._ortholog_clusterer = OrthologClusterer()
def setUp(self):
self._ortholog_clusterer = OrthologClusterer()
