def test_fish_rna(save_path):
gene_dataset_fish = SmfishDataset(save_path)
gene_dataset_seq = CortexDataset(save_path=save_path,
genes_fish=gene_dataset_fish.gene_names,
genes_to_keep=[],
additional_genes=50)
benchmark_fish_scrna(gene_dataset_seq, gene_dataset_fish)
def test_fish_rna(save_path):
gene_dataset_fish = SmfishDataset(save_path)
gene_dataset_seq = CortexDataset(
save_path=save_path,
genes_to_keep=gene_dataset_fish.gene_names,
total_genes=gene_dataset_fish.nb_genes + 50)
benchmark_fish_scrna(gene_dataset_seq, gene_dataset_fish)
def test_fish_rna():
gene_dataset_fish = SmfishDataset()
gene_dataset_seq = CortexDataset(genes_fish=gene_dataset_fish.gene_names,
genes_to_keep=[],
additional_genes=50)
benchamrk_fish_scrna(gene_dataset_seq, gene_dataset_fish)
def test_smfish():
smfish_dataset = SmfishDataset(save_path='tests/data/')
base_benchmark(smfish_dataset)
def test_populate(self):
dataset = SmfishDataset(use_high_level_cluster=False)
self.assertEqual(dataset.cell_types[0], "Excluded")
self.assertEqual(dataset.cell_types[1], "Pyramidal L6")
def test_train_one(self):
dataset = SmfishDataset(use_high_level_cluster=False)
unsupervised_training_one_epoch(dataset)