Loading deepchem/molnet/__init__.py +3 −0 Original line number Diff line number Diff line Loading @@ -28,6 +28,9 @@ from deepchem.molnet.load_function.toxcast_datasets import load_toxcast from deepchem.molnet.dnasim import simulate_motif_density_localization from deepchem.molnet.dnasim import simulate_motif_counting from deepchem.molnet.dnasim import simple_motif_embedding from deepchem.molnet.dnasim import motif_density from deepchem.molnet.dnasim import simulate_single_motif_detection from deepchem.molnet.run_benchmark import run_benchmark from deepchem.molnet.run_benchmark_low_data import run_benchmark_low_data deepchem/molnet/tests/test_dnasim.py +41 −5 Original line number Diff line number Diff line Loading @@ -7,7 +7,7 @@ class TestDNASim(unittest.TestCase): def test_motif_density_localization_simulation(self): "Test motif density localization simulation." "" motif_density_localization_simulation_parameters = { params = { "motif_name": "TAL1_known4", "seq_length": 1000, "center_size": 150, Loading @@ -18,13 +18,13 @@ class TestDNASim(unittest.TestCase): "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_motif_density_localization( **motif_density_localization_simulation_parameters) **params) assert sequences.shape == (60,) assert y.shape == (60, 1) def test_motif_counting_simulation(self): "Test motif counting" motif_count_simulation_parameters = { params = { "motif_name": "TAL1_known4", "seq_length": 1000, "pos_counts": [5, 10], Loading @@ -33,7 +33,43 @@ class TestDNASim(unittest.TestCase): "num_neg": 30, "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_motif_counting( **motif_count_simulation_parameters) sequences, y, embed = dc.molnet.simulate_motif_counting(**params) assert sequences.shape == (60,) assert y.shape == (60, 1) def test_simple_motif_embedding(self): "Test simple motif embedding" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_seqs": 30, "GC_fraction": 0.4 } sequences, embed = dc.molnet.simple_motif_embedding(**params) assert sequences.shape == (30,) def test_motif_density(self): "Test motif density" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_seqs": 30, "min_counts": 2, "max_counts": 4, "GC_fraction": 0.4 } sequences, embed = dc.molnet.motif_density(**params) assert sequences.shape == (30,) def test_single_motif_detection(self): "Test single motif detection" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_pos": 30, "num_neg": 30, "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_single_motif_detection(**params) assert sequences.shape == (60,) assert y.shape == (60, 1) setup.py +1 −8 Original line number Diff line number Diff line from setuptools import setup config = { 'install_requires': ['simdna==0.3'], 'dependency_links': ["https://github.com/kundajelab/simdna/tarball/0.3#egg=simdna-0.3"], 'setup_requires': ['pbr'], 'pbr': True } config = {'setup_requires': ['pbr'], 'pbr': True} setup(**config) Loading
deepchem/molnet/__init__.py +3 −0 Original line number Diff line number Diff line Loading @@ -28,6 +28,9 @@ from deepchem.molnet.load_function.toxcast_datasets import load_toxcast from deepchem.molnet.dnasim import simulate_motif_density_localization from deepchem.molnet.dnasim import simulate_motif_counting from deepchem.molnet.dnasim import simple_motif_embedding from deepchem.molnet.dnasim import motif_density from deepchem.molnet.dnasim import simulate_single_motif_detection from deepchem.molnet.run_benchmark import run_benchmark from deepchem.molnet.run_benchmark_low_data import run_benchmark_low_data
deepchem/molnet/tests/test_dnasim.py +41 −5 Original line number Diff line number Diff line Loading @@ -7,7 +7,7 @@ class TestDNASim(unittest.TestCase): def test_motif_density_localization_simulation(self): "Test motif density localization simulation." "" motif_density_localization_simulation_parameters = { params = { "motif_name": "TAL1_known4", "seq_length": 1000, "center_size": 150, Loading @@ -18,13 +18,13 @@ class TestDNASim(unittest.TestCase): "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_motif_density_localization( **motif_density_localization_simulation_parameters) **params) assert sequences.shape == (60,) assert y.shape == (60, 1) def test_motif_counting_simulation(self): "Test motif counting" motif_count_simulation_parameters = { params = { "motif_name": "TAL1_known4", "seq_length": 1000, "pos_counts": [5, 10], Loading @@ -33,7 +33,43 @@ class TestDNASim(unittest.TestCase): "num_neg": 30, "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_motif_counting( **motif_count_simulation_parameters) sequences, y, embed = dc.molnet.simulate_motif_counting(**params) assert sequences.shape == (60,) assert y.shape == (60, 1) def test_simple_motif_embedding(self): "Test simple motif embedding" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_seqs": 30, "GC_fraction": 0.4 } sequences, embed = dc.molnet.simple_motif_embedding(**params) assert sequences.shape == (30,) def test_motif_density(self): "Test motif density" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_seqs": 30, "min_counts": 2, "max_counts": 4, "GC_fraction": 0.4 } sequences, embed = dc.molnet.motif_density(**params) assert sequences.shape == (30,) def test_single_motif_detection(self): "Test single motif detection" params = { "motif_name": "TAL1_known4", "seq_length": 1000, "num_pos": 30, "num_neg": 30, "GC_fraction": 0.4 } sequences, y, embed = dc.molnet.simulate_single_motif_detection(**params) assert sequences.shape == (60,) assert y.shape == (60, 1)
setup.py +1 −8 Original line number Diff line number Diff line from setuptools import setup config = { 'install_requires': ['simdna==0.3'], 'dependency_links': ["https://github.com/kundajelab/simdna/tarball/0.3#egg=simdna-0.3"], 'setup_requires': ['pbr'], 'pbr': True } config = {'setup_requires': ['pbr'], 'pbr': True} setup(**config)
