def test_IgorModel_Parms(self):
species = "human"
chain = "tcr_beta"
mdl_parms = IgorModel_Parms()
fln_model_parms, fln_model_marginals = get_default_models_paths_species_chain(
species, chain)
self.assertTrue(os.path.isfile(fln_model_parms))
mdl_parms.read_model_parms(fln_model_parms)
self.assertFalse(
'anchor_index' in mdl_parms.df_V_ref_genome.columns.to_list())
self.assertFalse(
'anchor_index' in mdl_parms.df_J_ref_genome.columns.to_list())
fln_dict = get_default_fln_dict_ref_genomes_species_chain(
species, chain)
self.assertTrue(os.path.isfile(fln_dict["fln_V_gene_CDR3_anchors"]))
self.assertTrue(os.path.isfile(fln_dict["fln_J_gene_CDR3_anchors"]))
mdl_parms.attach_V_anchors_from_file(
fln_dict["fln_V_gene_CDR3_anchors"])
mdl_parms.attach_J_anchors_from_file(
fln_dict["fln_J_gene_CDR3_anchors"])
self.assertTrue(
'anchor_index' in mdl_parms.df_V_ref_genome.columns.to_list())
self.assertTrue(
'anchor_index' in mdl_parms.df_J_ref_genome.columns.to_list())
def test_IgorModel_Parms_get_IgorRefGenome_VJ(self):
"""
Return an IgorRefGenome object generated from GeneChoice events
and use it to write a ref_genome directory that will be use to run IGoR.
"""
species = "human"
chain = "tcr_alpha"
fln_model_parms, fln_model_marginals = get_default_models_paths_species_chain(
species, chain)
fln_dict = get_default_fln_dict_ref_genomes_species_chain(
species, chain)
# 1. Make an IgorModel_Parms from scratch
mdl_parms = IgorModel_Parms(
model_parms_file=fln_model_parms,
fln_V_gene_CDR3_anchors=fln_dict["fln_V_gene_CDR3_anchors"],
fln_J_gene_CDR3_anchors=fln_dict["fln_J_gene_CDR3_anchors"])
self.assertTrue(mdl_parms.event_GeneChoice_D is None)
self.assertTrue(mdl_parms.df_D_ref_genome is None)
# 2. Get IgorRefGenome from events
ref_genome = mdl_parms.get_IgorRefGenome()
# 3. Write a ref_genome_dir
tmp_ref_genome_dir = tempfile.TemporaryDirectory(dir='.',
prefix="ref_genome")
ref_genome.write_ref_genome_dir(tmp_ref_genome_dir.name)
fln_tmp_dict = dict()
fln_tmp_dict[
'fln_genomicVs'] = tmp_ref_genome_dir.name + "/" + "genomicVs.fasta"
fln_tmp_dict[
'fln_genomicJs'] = tmp_ref_genome_dir.name + "/" + "genomicJs.fasta"
fln_tmp_dict[
'fln_V_gene_CDR3_anchors'] = tmp_ref_genome_dir.name + "/" + "V_gene_CDR3_anchors.csv"
fln_tmp_dict[
'fln_J_gene_CDR3_anchors'] = tmp_ref_genome_dir.name + "/" + "J_gene_CDR3_anchors.csv"
self.assertTrue(os.path.isfile(fln_tmp_dict["fln_genomicVs"]))
self.assertTrue(os.path.isfile(fln_tmp_dict["fln_genomicJs"]))
self.assertTrue(os.path.isfile(
fln_tmp_dict["fln_V_gene_CDR3_anchors"]))
self.assertTrue(os.path.isfile(
fln_tmp_dict["fln_J_gene_CDR3_anchors"]))
self.assertFalse(
os.path.isfile(tmp_ref_genome_dir.name + "/" + "genomicDs.fasta"))
tmp_ref_genome_dir.cleanup()
def test_IgorModel_Parms_from_dataframe(self):
mdl_hb = get_default_IgorModel("human", "tcr_beta")
import copy
genomic_dict = copy.deepcopy(mdl_hb.genomic_dataframe_dict)
genomic_dict['V']['name'] = v_genLabel(genomic_dict['V']['name'])
genomic_dict['J']['name'] = v_genLabel(genomic_dict['J']['name'])
new_V_gene_dict = {
'name': 'my_pseudo_TRBV',
'value':
'AAACCCTTTGGGACCCAGAGCCCAAGACACAAGATCACAGAGACAGGAAGGCAGGTGACCTTGGCGTGTCACCAGACTTGGAACCACAACAATATGTTCTGGTATCGACAAGACCTGGGACATGGGCTGAGGCTGATCCATTACTCATATGGTGTTCACGACACTAACAAAGGAGAAGTCTCAGATGGCTACAGTGTCTCTAGATCAAACACAGAGGACCTCCCCCTCACTCTGTAGTCTGCTGCCTCCTCCCAGACATCTGTATATTTCTGCGCCAGCAGTGAGTC',
'anchor_index': 270
}
df_V = genomic_dict['V'].loc[10:15]
df_V = df_V.append(new_V_gene_dict, ignore_index=True)
df_V.index.name = 'id'
df_V
mdl_parms_0 = IgorModel_Parms.make_default_VDJ(df_V, genomic_dict['D'],
genomic_dict['J'])
mdl_marginals_0 = IgorModel_Marginals.make_uniform_from_parms(
mdl_parms_0)
print("parms.Edges: ")
print(mdl_hb.parms.Edges)
print(mdl_parms_0.Edges)
print("parms.Edges_dict:")
print(mdl_hb.parms.Edges_dict)
print(mdl_parms_0.Edges_dict)
print("marginals.network_dict")
print(mdl_hb.marginals.network_dict)
print(mdl_marginals_0.network_dict)
self.assertIsInstance(mdl_parms_0, IgorModel_Parms)
def test_get_df_ref_genome_from_files(self):
ofile_mock_VDJ_fln_genomicVs = io.StringIO(str_mock_VDJ_fln_genomicVs)
ofile_mock_VDJ_fln_V_gene_CDR3_anchors = io.StringIO(
str_mock_VDJ_fln_V_gene_CDR3_anchors)
ofile_mock_VDJ_fln_genomicDs = io.StringIO(str_mock_VDJ_fln_genomicDs)
ofile_mock_VDJ_fln_genomicJs = io.StringIO(str_mock_VDJ_fln_genomicJs)
ofile_mock_VDJ_fln_J_gene_CDR3_anchors = io.StringIO(
str_mock_VDJ_fln_J_gene_CDR3_anchors)
df_V_ref_genome = get_dataframe_from_fasta_and_csv_anchors(
ofile_mock_VDJ_fln_genomicVs,
ofile_mock_VDJ_fln_V_gene_CDR3_anchors)
df_D_ref_genome = get_dataframe_from_fasta_and_csv_anchors(
ofile_mock_VDJ_fln_genomicDs)
df_J_ref_genome = get_dataframe_from_fasta_and_csv_anchors(
ofile_mock_VDJ_fln_genomicJs,
ofile_mock_VDJ_fln_J_gene_CDR3_anchors)
self.assertIsInstance(df_V_ref_genome, pd.DataFrame)
self.assertIsInstance(df_D_ref_genome, pd.DataFrame)
self.assertIsInstance(df_J_ref_genome, pd.DataFrame)
mdl_parms = IgorModel_Parms.make_default_VDJ(df_V_ref_genome,
df_D_ref_genome,
df_J_ref_genome)
self.assertIsInstance(mdl_parms, IgorModel_Parms)
def test_IgorModel_Parms_get_IgorRefGenome_VDJ(self):
species = "human"
chain = "tcr_beta"
fln_model_parms, fln_model_marginals = get_default_models_paths_species_chain(
species, chain)
fln_dict = get_default_fln_dict_ref_genomes_species_chain(
species, chain)
mdl_parms = IgorModel_Parms(
model_parms_file=fln_model_parms,
fln_V_gene_CDR3_anchors=fln_dict["fln_V_gene_CDR3_anchors"],
fln_J_gene_CDR3_anchors=fln_dict["fln_J_gene_CDR3_anchors"])
self.assertFalse(mdl_parms.df_V_anchors is None)
self.assertFalse(mdl_parms.df_J_anchors is None)
self.assertFalse(mdl_parms.event_GeneChoice_D is None)
self.assertFalse(mdl_parms.df_D_ref_genome is None)
ref_genome = mdl_parms.get_IgorRefGenome()
mdl_parms.gen_EventDict_DataFrame()
tmp_ref_genome_dir = tempfile.TemporaryDirectory(dir='.',
prefix="ref_genome")
ref_genome.write_ref_genome_dir(tmp_ref_genome_dir.name)
print(ref_genome.to_dict())
fln_tmp_dict = dict()
fln_tmp_dict[
'fln_genomicVs'] = tmp_ref_genome_dir.name + "/" + "genomicVs.fasta"
fln_tmp_dict[
'fln_genomicDs'] = tmp_ref_genome_dir.name + "/" + "genomicDs.fasta"
fln_tmp_dict[
'fln_genomicJs'] = tmp_ref_genome_dir.name + "/" + "genomicJs.fasta"
fln_tmp_dict[
'fln_V_gene_CDR3_anchors'] = tmp_ref_genome_dir.name + "/" + "V_gene_CDR3_anchors.csv"
fln_tmp_dict[
'fln_J_gene_CDR3_anchors'] = tmp_ref_genome_dir.name + "/" + "J_gene_CDR3_anchors.csv"
# time.sleep(20)
self.assertTrue(os.path.isfile(fln_tmp_dict["fln_genomicVs"]))
self.assertTrue(os.path.isfile(fln_tmp_dict["fln_genomicDs"]))
self.assertTrue(os.path.isfile(fln_tmp_dict["fln_genomicJs"]))
self.assertTrue(os.path.isfile(
fln_tmp_dict["fln_V_gene_CDR3_anchors"]))
self.assertTrue(os.path.isfile(
fln_tmp_dict["fln_J_gene_CDR3_anchors"]))
tmp_ref_genome_dir.cleanup()
def test_IgorModel_write_model(self):
mdl_hb = IgorModel.load_default("human", "tcr_beta")
fln_model_parms = 'model_parms.txt'
fln_model_marginals = 'model_marginals.txt'
fln_V_gene_CDR3_anchors = 'V_gene_CDR3_anchors.csv'
fln_J_gene_CDR3_anchors = 'J_gene_CDR3_anchors.csv'
## TODO: ADD anchors
mdl_hb.write_model(fln_model_parms, fln_model_marginals,
fln_V_gene_CDR3_anchors, fln_J_gene_CDR3_anchors)
mdl_hb_2 = IgorModel(fln_model_parms,
fln_model_marginals,
fln_V_gene_CDR3_anchors=fln_V_gene_CDR3_anchors,
fln_J_gene_CDR3_anchors=fln_J_gene_CDR3_anchors)
# TODO: CHANGE ANCHORS WITH DATAFRAME.
mdl_hb_2
# FIXME: SOLVE THE REFERENCES TO ANCHORS AND SEQUENCES NAMES PROBLEM
# mdl_hb.parms.df_V_ref_genome
print("mdl_hb_2.parms.dictNameNickname: ",
mdl_hb_2.parms.dictNameNickname)
df = mdl_hb_2.get_event_realizations_DataFrame('j_choice')
print("mdl_hb_2.genomic_dataframe_dict: ",
mdl_hb_2.genomic_dataframe_dict)
new_df = df[:4]
mdl_hb_2.parms.gen_NameNickname_dict()
mdl_hb_2.set_realization_event_from_DataFrame('j_choice', new_df)
mdl_hb_2.set_event_realizations_from_DataFrame('j_choice', new_df)
print("mdl_hb_2.parms.dictNameNickname: ",
mdl_hb_2.parms.dictNameNickname)
mdl_copy.set_genomic_dataframe_dict()
mdl_parms = IgorModel_Parms()
mdl_parms.Event_list # add_event() #add_Event()
# import copy
# mdl_copy = copy.deepcopy(mdl_hb)
# mdl_copy
# mdl_hb.parms.df_V_ref_genome
# v_genLabel(mdl_hb.parms.df_V_ref_genome['name'])
# print(mdl_hb_2.parms.df_V_ref_genome)
# mdl_hb_2.genomic_dataframe_dict
self.assertIsInstance(mdl_hb_2, IgorModel)
self.assertTrue(os.path.isfile(fln_model_parms))
self.assertTrue(os.path.isfile(fln_model_marginals))
self.assertTrue(os.path.isfile(fln_V_gene_CDR3_anchors))
self.assertTrue(os.path.isfile(fln_J_gene_CDR3_anchors))
cmd = "rm {} {} {} {}".format(fln_model_parms, fln_model_marginals,
fln_V_gene_CDR3_anchors,
fln_J_gene_CDR3_anchors)
p = subprocess.run(cmd, shell=True, capture_output=True, text=True)
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_IgorModel_Parms_with_anchors(self):
species = "human"
chain = "tcr_beta"
fln_model_parms, fln_model_marginals = get_default_models_paths_species_chain(
species, chain)
fln_dict = get_default_fln_dict_ref_genomes_species_chain(
species, chain)
print("fln_dict: ", fln_dict)
mdl_parms = IgorModel_Parms(
model_parms_file=fln_model_parms,
fln_V_gene_CDR3_anchors=fln_dict["fln_V_gene_CDR3_anchors"],
fln_J_gene_CDR3_anchors=fln_dict["fln_J_gene_CDR3_anchors"])
# no function in anchors file
self.assertTrue(
'anchor_index' in mdl_parms.df_V_ref_genome.columns.to_list())
self.assertTrue(
'anchor_index' in mdl_parms.df_J_ref_genome.columns.to_list())