def test_targets_SPI1_PAX5(self):
# https://github.com/YosefLab/epitome/issues/22
with warnings.catch_warnings(record=True) as warning_list:
warnings.simplefilter('always')
matrix, cellmap, targetmap = EpitomeDataset.get_assays(targets = ['DNase','SPI1', 'PAX5'],min_cells_per_target=2, min_targets_per_cell=2)
self.assertTrue(len(warning_list) == 1) # one for SPI1 and PAX5
self.assertTrue(all(item.category == UserWarning for item in warning_list))
def test_gets_correct_matrix_indices(self):
eligible_cells = ['IMR-90','H1','H9']
eligible_targets = ['DNase','H4K8ac']
matrix, cellmap, targetmap = EpitomeDataset.get_assays(
targets = eligible_targets,
cells = eligible_cells, min_cells_per_target = 3, min_targets_per_cell = 1)
self.assertTrue(matrix[cellmap['IMR-90']][targetmap['H4K8ac']]==0) # data for first row
def test_get_assays_single_target(self):
TF = ['DNase', 'JUND']
matrix, cellmap, targetmap = EpitomeDataset.get_assays(targets = TF,
min_cells_per_target = 2,
min_targets_per_cell = 2)
targets = list(targetmap)
# Make sure only JUND and DNase are in list of targets
self.assertTrue(len(targets) == 2)
for t in TF:
self.assertTrue(t in targets)
def test_get_assays_without_DNase(self):
TF = 'JUND'
matrix, cellmap, targetmap = EpitomeDataset.get_assays(targets = TF,
similarity_targets = ['H3K27ac'],
min_cells_per_target = 2,
min_targets_per_cell = 1)
targets = list(targetmap)
# Make sure only JUND and is in list of assays
self.assertTrue(len(targets) == 2)
self.assertTrue(TF in targets)
self.assertTrue('H3K27ac' in targets)
