Python load_references Examples

Example #1

File: test_dissimilarity.py Project: TRON-Bioinformatics/neofox

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references()
     self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
     self.runner = Runner()
     self.proteome_blastp_runner = BlastpRunner(
         runner=self.runner, configuration=self.configuration,
         database=os.path.join(self.references.proteome_db, "homo_sapiens"))

Example #2

 def setUp(self):
     references, self.configuration = integration_test_tools.load_references(organism=ORGANISM_MUS_MUSCULUS)
     self.runner = Runner()
     self.available_alleles = references.get_available_alleles()
     self.test_mhc_one = integration_test_tools.get_h2_one_test(references.get_mhc_database())
     self.test_mhc_two = integration_test_tools.get_h2_two_test(references.get_mhc_database())
     self.mhc_parser = MhcParser.get_mhc_parser(references.get_mhc_database())
     self.proteome_blastp_runner = BlastpRunner(
         runner=self.runner, configuration=self.configuration,
         database=references.get_proteome_database())

Example #3

File: test_prime.py Project: TRON-Bioinformatics/neofox

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references(
     )
     self.runner = Runner()
     self.prime = Prime(runner=self.runner,
                        configuration=self.configuration,
                        mhc_parser=HlaParser(
                            self.references.get_mhc_database()))
     self.hla_database = self.references.get_mhc_database()
     self.test_mhc_one = integration_test_tools.get_hla_one_test(
         self.hla_database)
     self.uniprot = Uniprot(self.references.uniprot_pickle)

Example #4

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references()
     self.runner = Runner()
     mhc_parser = MhcParser.get_mhc_parser(self.references.get_mhc_database())
     self.mixmhcpred = MixMHCpred(
         runner=self.runner, configuration=self.configuration, mhc_parser=mhc_parser
     )
     self.mixmhc2pred = MixMhc2Pred(
         runner=self.runner, configuration=self.configuration, mhc_parser=mhc_parser
     )
     self.hla_database = self.references.get_mhc_database()
     self.test_mhc_one = integration_test_tools.get_hla_one_test(self.hla_database)
     self.test_mhc_two = integration_test_tools.get_hla_two_test(self.hla_database)
     self.uniprot = Uniprot(self.references.uniprot_pickle)

Example #5

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references(
     )
     self.references_mouse, self.configuration_mouse = integration_test_tools.load_references(
         organism=ORGANISM_MUS_MUSCULUS)
     # self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
     # self.runner = Runner()
     self.patient_id = "Pt29"
     input_file = pkg_resources.resource_filename(
         neofox.tests.__name__, "resources/test_candidate_file.txt")
     patients_file = pkg_resources.resource_filename(
         neofox.tests.__name__, "resources/test_patient_file.txt")
     patients_file_mouse = pkg_resources.resource_filename(
         neofox.tests.__name__, "resources/test_patient_file_mouse.txt")
     self.hla_database = self.references.get_mhc_database()
     self.h2_database = self.references_mouse.get_mhc_database()
     self.patients = ModelConverter.parse_patients_file(
         patients_file, self.hla_database)
     self.patients_mouse = ModelConverter.parse_patients_file(
         patients_file_mouse, self.h2_database)
     self.neoantigens = ModelConverter.parse_candidate_file(input_file)
     self.neoantigens_mouse = ModelConverter.parse_candidate_file(
         input_file)

Example #6

 def setUp(self):
     references, self.configuration = integration_test_tools.load_references(
     )
     self.runner = Runner()
     self.available_alleles_mhc1 = (
         references.get_available_alleles().get_available_mhc_i())
     self.available_alleles_mhc2 = (
         references.get_available_alleles().get_available_mhc_ii())
     self.hla_database = references.get_mhc_database()
     self.mhc_parser = MhcParser.get_mhc_parser(self.hla_database)
     self.test_mhc_one = integration_test_tools.get_hla_one_test(
         self.hla_database)
     self.test_mhc_two = integration_test_tools.get_hla_two_test(
         self.hla_database)
     self.uniprot = Uniprot(references.uniprot_pickle)
     self.proteome_blastp_runner = BlastpRunner(
         runner=self.runner,
         configuration=self.configuration,
         database=references.get_proteome_database())

Example #7

 def _load_references(self):
     references, configuration = integration_test_tools.load_references()
     fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
     return references, configuration, fastafile

Example #8

File: test_neoag.py Project: TRON-Bioinformatics/neofox

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references(
     )
     self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file(
     )
     self.runner = Runner()

Example #9

File: test_hex.py Project: TRON-Bioinformatics/neofox

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references()
     self.runner = Runner()

Example #10

File: test_synthetic_data.py Project: TRON-Bioinformatics/neofox

 def setUp(self):
     self.references, self.configuration = integration_test_tools.load_references()
     self.data_generator = DataGenerator(self.references, self.configuration)