class TestBlast(TestCase):
def setUp(self):
self.references, self.configuration, self.fastafile = self._load_references(
)
self.proteome_blastp_runner = BlastpRunner(
runner=Runner(verbose=False),
configuration=self.configuration,
database=self.references.get_proteome_database())
self.iedb_blastp_runner = BlastpRunner(
runner=Runner(verbose=False),
configuration=self.configuration,
database=self.references.get_iedb_database())
def _load_references(self):
references, configuration = integration_test_tools.load_references()
fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
return references, configuration, fastafile
def test_blast(self):
sequence = "FIAGLIAIV"
res = self.proteome_blastp_runner.get_most_similar_wt_epitope(sequence)
self.assertIsNotNone(res)
self.assertEqual('FVAGLIVLL', res)
def test_calculate_similarity_database(self):
sequence = "FIAGLIAIV"
res = self.iedb_blastp_runner.calculate_similarity_database(sequence)
self.assertIsNotNone(res)
self.assertEqual(1.0, res)
def test_performance_most_similar_wt_epitope(self):
times = []
for k in [9, 15, 25, 50]:
for _ in range(10):
kmer = integration_test_tools.get_random_kmer(k=9)
start = time.time()
similar_wt = self.proteome_blastp_runner.get_most_similar_wt_epitope(
kmer)
times.append(time.time() - start)
logger.info("{}: {}".format(kmer, similar_wt))
logger.info("Average time for {}-mers: {}".format(
k, np.mean(times)))
logger.info("Standard deviation for {}-mers: {}".format(
k, np.std(times)))
def test_performance_calculate_similarity_database(self):
times = []
for k in [9, 15, 25, 50]:
for _ in range(10):
kmer = integration_test_tools.get_random_kmer(k=9)
start = time.time()
similarity = self.proteome_blastp_runner.calculate_similarity_database(
kmer)
times.append(time.time() - start)
logger.info("{}: {}".format(kmer, similarity))
logger.info("Average time for {}-mers: {}".format(
k, np.mean(times)))
logger.info("Standard deviation for {}-mers: {}".format(
k, np.std(times)))
def setUp(self):
self.references, self.configuration, self.fastafile = self._load_references(
)
self.proteome_blastp_runner = BlastpRunner(
runner=Runner(verbose=False),
configuration=self.configuration,
database=self.references.get_proteome_database())
self.iedb_blastp_runner = BlastpRunner(
runner=Runner(verbose=False),
configuration=self.configuration,
database=self.references.get_iedb_database())
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"))
def setUp(self):
self.references, self.configuration, self.fastafile = self._load_references(
)
self.iedb_blastp_runner = BlastpRunner(
runner=Runner(verbose=False),
configuration=self.configuration,
database=self.references.get_iedb_database())
self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(
iedb_blastp_runner=self.iedb_blastp_runner)
def __init__(
self,
references: ReferenceFolder,
configuration: DependenciesConfiguration,
tcell_predictor: TcellPrediction,
self_similarity: SelfSimilarityCalculator,
affinity_threshold =neofox.AFFINITY_THRESHOLD_DEFAULT
):
"""class to annotate neoantigens"""
self.runner = Runner()
self.configuration = configuration
self.proteome_db = references.proteome_db
self.available_alleles = references.get_available_alleles()
self.tcell_predictor = tcell_predictor
self.self_similarity = self_similarity
self.organism = references.organism
# NOTE: this one loads a big file, but it is faster loading it multiple times than passing it around
self.uniprot = Uniprot(references.uniprot_pickle)
# initialise proteome and IEDB BLASTP runners
self.proteome_blastp_runner = BlastpRunner(
runner=self.runner, configuration=configuration,
database=references.get_proteome_database())
self.iedb_blastp_runner = BlastpRunner(
runner=self.runner, configuration=configuration,
database=references.get_iedb_database())
# NOTE: these resources do not read any file thus can be initialised fast
self.dissimilarity_calculator = DissimilarityCalculator(
proteome_blastp_runner=self.proteome_blastp_runner, affinity_threshold=affinity_threshold)
self.neoantigen_fitness_calculator = NeoantigenFitnessCalculator(iedb_blastp_runner=self.iedb_blastp_runner)
self.neoag_calculator = NeoagCalculator(
runner=self.runner, configuration=configuration, affinity_threshold=affinity_threshold
)
self.differential_binding = DifferentialBinding(affinity_threshold=affinity_threshold)
self.priority_score_calculator = PriorityScore()
self.iedb_immunogenicity = IEDBimmunogenicity(affinity_threshold=affinity_threshold)
self.amplitude = Amplitude()
self.hex = Hex(runner=self.runner, configuration=configuration, references=references)
self.mhc_database = references.get_mhc_database()
self.mhc_parser = MhcParser.get_mhc_parser(self.mhc_database)
self.resources_versions = references.get_resources_versions()
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())
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())