def test_something(self):
self.assertEqual(p3.rcParams['paths.igor_exec'], None)
mdl_hb = p3.IgorModel.load_default('human', 'tcr_beta')
self.assertIsInstance(mdl_hb, p3.IgorModel)
p3.rcParams['paths.igor_exec'] = 'mygor'
df_seqs = p3.generate(10, mdl_hb)
self.assertIsInstance(df_seqs, pd.DataFrame)
def test_one_sequence_evaluate(self):
hb_mdl = get_default_IgorModel("human", "tcr_beta")
self.assertIsInstance(hb_mdl, IgorModel)
sequences = generate(10, hb_mdl)
self.assertIsInstance(sequences, pd.DataFrame)
ref_genome = get_IgorRefGenome_VDJ_from_IMGT("H**o+sapiens", "TRB")
self.assertIsInstance(ref_genome, IgorRefGenome)
ref_genome.clean_empty_anchors()
self.assertIsInstance(ref_genome, IgorRefGenome)
mdl_ini = IgorModel.make_default_model_from_IgorRefGenome(ref_genome)
self.assertIsInstance(mdl_ini, IgorModel)
mdl_new, df_likelihood = infer(sequences, mdl_ini)
one_sequence = 'GGTGCTGTCGTCTCTCAACATCCGAGCTGGGTTATCTGTAAGAGTGGAACCTCTGTGAAGATCGAGTGCCGTTCCCTGGACTTTCAGGCCACAACTATGTTTTGGTATCGTCAGTTCCCGAAACAGAGTCTCATGCTGATGGCAACTTCCAATGAGGGCTCCAAGGCCACATACGAGCAAGGCGTCGAGAAGGACAAGTTTCTCATCAACCATGCAAGCCTGACCTTGTCCACTCTGACAGTGACCAGTGCCCATCCTGAAGACAGCAGCTTCTACATCTGCAGTGCTCAGTTCGCGGGAATTAGGAACACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG'
one_pgen = evaluate(one_sequence, mdl_new, N_scenarios=5)
print(one_pgen)
def test_from_generation_to_evaluation(self):
hb_mdl = get_default_IgorModel("human", "tcr_beta")
self.assertIsInstance(hb_mdl, IgorModel)
sequences = generate(10, hb_mdl)
self.assertIsInstance(sequences, pd.DataFrame)
ref_genome = get_IgorRefGenome_VDJ_from_IMGT("H**o+sapiens", "TRB")
self.assertIsInstance(ref_genome, IgorRefGenome)
ref_genome.clean_empty_anchors()
self.assertIsInstance(ref_genome, IgorRefGenome)
mdl_ini = IgorModel.make_default_model_from_IgorRefGenome(ref_genome)
self.assertIsInstance(mdl_ini, IgorModel)
mdl_new, df_likelihood = infer(sequences, mdl_ini)
self.assertIsInstance(mdl_new, IgorModel)
self.assertIsInstance(df_likelihood, pd.DataFrame)
def setUp(self) -> None:
self.species = "human"
self.chain = "tcr_beta"
self.mdl = IgorModel.load_default(self.species, self.chain)
# mdl = IgorTask.run_generate(return_df=True)
self.pd_sequences = generate(10, self.mdl)
def test_generate(self):
df = generate(10, mdl=self.mdl)
self.assertIsInstance(df, pd.DataFrame)
self.assertTrue(len(df) == 10)
def test_pygor_generate(self):
mdl = get_default_IgorModel("human", "tcr_beta")
df_seqs = generate(10, mdl)
print(df_seqs)