def test_IgorRefGenome_from_imgt(self):
print(IgorRefGenome.get_imgt_list_species())
hs_trb_imgt_ref_genome = IgorRefGenome.load_VDJ_from_IMGT_website(
"H**o+sapiens", "TRB")
self.assertIsInstance(hs_trb_imgt_ref_genome, IgorRefGenome)
hs_tra_imgt_ref_genome = IgorRefGenome.load_VJ_from_IMGT_website(
"H**o+sapiens", "TRA")
self.assertIsInstance(hs_tra_imgt_ref_genome, IgorRefGenome)
def test_IgorRefGenome_default(self):
species = "human"
chain = "tcr_beta"
ref_genome_files_dict = get_default_fln_dict_ref_genomes_species_chain(
species, chain)
genomes = IgorRefGenome(**ref_genome_files_dict)
genomes_default = IgorRefGenome.load_default(species, chain)
self.assertEqual(genomes.V.loc[0].values[0],
genomes_default.V.loc[0].values[0])
self.assertEqual(genomes.V.loc[0].values[1],
genomes_default.V.loc[0].values[1])
def test_IgorRefGenome(self):
ref_geno = IgorRefGenome()
ref_geno.path_ref_genome = self.ref_genome_path_dir
ref_geno.update_fln_names(path_ref_genome=ref_geno.path_ref_genome)
ref_geno.load_dataframes_from_ref_genome_files()
print(ref_geno.to_dict())
# Check equality of properties
self.assertTrue(True, True)
def test_IgorRefGenome_write_ref_genome(self):
# 1. Make a temporal directory
tmp_test_dir = tempfile.TemporaryDirectory(".", prefix="testando")
species = "human"
chain = "tcr_beta"
# 2. load default RefGenome
genomes = IgorRefGenome.load_default(species, chain)
print(genomes.df_genomicVs)
print(genomes.df_V_anchors)
print(genomes.df_V_ref_genome)
# 3. write ref_genome in temporary directory.
genomes.write_ref_genome_dir(tmp_test_dir.name)
# 4. Assert if files in directory
tmp_test_fln_dict = dict()
tmp_test_fln_dict[
'fln_genomicVs'] = tmp_test_dir.name + "/" + "genomicVs.fasta"
tmp_test_fln_dict[
'fln_genomicDs'] = tmp_test_dir.name + "/" + "genomicDs.fasta"
tmp_test_fln_dict[
'fln_genomicJs'] = tmp_test_dir.name + "/" + "genomicJs.fasta"
tmp_test_fln_dict[
'fln_V_gene_CDR3_anchors'] = tmp_test_dir.name + "/" + "V_gene_CDR3_anchors.csv"
tmp_test_fln_dict[
'fln_J_gene_CDR3_anchors'] = tmp_test_dir.name + "/" + "J_gene_CDR3_anchors.csv"
for fln_key in self.fln_dict.keys():
self.assertTrue(os.path.isfile(tmp_test_fln_dict[fln_key]))
# 5. Remove temporal directory.
tmp_test_dir.cleanup()
def test_IgorModel_from_dataframes(self):
ref_genome = IgorRefGenome.load_from_path(self.ref_genome_path_dir)
# Because the model depends has VDJ genes
self.assertIsInstance(ref_genome, IgorRefGenome)
mdl_from_ref_genome = IgorModel.make_default_model_from_IgorRefGenome(
ref_genome)
self.assertIsInstance(mdl_from_ref_genome, IgorModel)
print("mdl_from_ref_genome.V_anchors: ", mdl_from_ref_genome.V_anchors)
print("mdl_from_ref_genome.J_anchors: ", mdl_from_ref_genome.J_anchors)
path_mdl_data = self.tmp_dir.name + "/batch_mdldata"
aaa = path_mdl_data + "/ref_genome"
mdl_from_ref_genome
mdl_from_ref_genome.write_mdldata_dir()
ref_genome_again = mdl_from_ref_genome.parms.get_IgorRefGenome()
self.assertIsInstance(ref_genome_again, IgorRefGenome)
os.system("mkdir -p " + aaa)
ref_genome_again.write_ref_genome_dir(aaa)
fln_dict_tmp = get_default_ref_genome_fln_paths(ref_genome_path=aaa)
print(fln_dict_tmp, str_mock_VDJ_fln_dict.keys())
for fln_key in str_mock_VDJ_fln_dict.keys():
print("fln_dict_tmp[" + fln_key + "]:", fln_dict_tmp[fln_key])
self.assertTrue(os.path.isfile(fln_dict_tmp[fln_key]))
"""
def test_IgorModel_Parms_from_IgorRefGenome(self):
ref_genome = IgorRefGenome.load_default("human", "tcr_alpha")
self.assertIsInstance(ref_genome, IgorRefGenome)
ref_genome_dict = ref_genome.to_dict()
print(ref_genome.df_genomicVs)
print(ref_genome.df_V_anchors)
print(IgorRefGenome.V)
mdl_parms = IgorModel_Parms.make_default_VDJ_from_IgorRefGenome(
ref_genome)
def test_IgorRefGenome_from_path(self):
ref_genome = IgorRefGenome.load_from_path(self.ref_genome_path_dir)
ref_genome.load_J_anchors_from_file(ref_genome.fln_J_gene_CDR3_anchors)
print(ref_genome.df_J_anchors)
row = ref_genome.df_J_ref_genome.loc[9]
# print(row)
self.assertEqual(row['name'], "TRBJ2-2P*01")
self.assertEqual(row['value'],
"CTGAGAGGCGCTGCTGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG")
self.assertTrue(np.isnan(row['anchor_index']))
self.assertTrue(np.isnan(row['function']))
def test_IgorRefGenome_clean_empty_anchors(self):
ref_genome = IgorRefGenome.load_from_path(self.ref_genome_path_dir)
row_9 = ref_genome.df_J_ref_genome.loc[9].copy()
row_10 = ref_genome.df_J_ref_genome.loc[10].copy()
self.assertEqual(row_9['name'], "TRBJ2-2P*01")
self.assertEqual(row_9['value'],
"CTGAGAGGCGCTGCTGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG")
self.assertTrue(np.isnan(row_9['anchor_index']))
self.assertTrue(np.isnan(row_9['function']))
ref_genome.clean_empty_anchors()
row_new_9 = ref_genome.df_J_ref_genome.loc[9].copy()
self.assertEqual(row_10['name'], row_new_9['name'])
self.assertEqual(row_10['value'], row_new_9['value'])
self.assertEqual(row_10['anchor_index'], row_new_9['anchor_index'])
self.assertEqual(row_10['function'], row_new_9['function'])
def test_infer_VJ(self):
# 0. Get your input sequences, in this case generated sequences
print(self.pd_sequences)
self.assertIsInstance(self.pd_sequences, pd.DataFrame)
# 1. Get an IgorRefGenome from imgt website
hb_ref_genome = IgorRefGenome.load_VJ_from_IMGT_website(
"H**o+sapiens", "TRB")
hb_ref_genome.clean_empty_anchors()
self.assertIsInstance(hb_ref_genome, IgorRefGenome)
# 2. Create a Model from a recently downloaded imgt models
hb_mdl_ini = IgorModel.make_default_model_from_IgorRefGenome(
hb_ref_genome)
self.assertIsInstance(hb_mdl_ini, IgorModel)
# 3. infer a new model using the initial model.
new_mdl = infer(self.pd_sequences, hb_mdl_ini, batch_clean=False)
self.assertIsInstance(new_mdl, IgorModel)
def test_IgorRefGenome_from_dataframe_genomics_dict(self):
ref_genome_pd_dict = dict()
ref_genome_pd_dict['V'] = get_dataframe_from_fasta_and_csv_anchors(
self.fln_dict['fln_genomicVs'],
self.fln_dict['fln_V_gene_CDR3_anchors'])
ref_genome_pd_dict['J'] = get_dataframe_from_fasta_and_csv_anchors(
self.fln_dict['fln_genomicJs'],
self.fln_dict['fln_J_gene_CDR3_anchors'])
ref_genome_pd_dict['D'] = get_dataframe_from_fasta_and_csv_anchors(
self.fln_dict['fln_genomicDs'])
ref_genome = IgorRefGenome.load_from_dataframe_genomics_dict(
ref_genome_pd_dict)
row = ref_genome.df_J_ref_genome.loc[9]
self.assertEqual(row['name'], "TRBJ2-2P*01")
self.assertEqual(row['value'],
"CTGAGAGGCGCTGCTGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG")
self.assertTrue(np.isnan(row['anchor_index']))
self.assertTrue(np.isnan(row['function']))