def _mixmhcprediction(
self, mhc_alleles: List[str], potential_ligand_sequences
) -> pd.DataFrame:
"""
Performs MixMHCpred prediction for desired hla allele and writes result to temporary file.
"""
outtmp = intermediate_files.create_temp_file(prefix="mixmhcpred", suffix=".txt")
tmpfasta = intermediate_files.create_temp_fasta(
potential_ligand_sequences, prefix="tmp_sequence_"
)
command = [
self.configuration.mix_mhc_pred,
"-a",
",".join(mhc_alleles),
"-i",
tmpfasta,
"-o",
outtmp,
]
self.runner.run_command(
cmd=command
)
try:
results = pd.read_csv(outtmp, sep="\t", comment="#")
except EmptyDataError:
message = "Results from MixMHCpred are empty, something went wrong [{}]. MHC I alleles {}, ligands {}".format(
" ".join(command), ",".join(mhc_alleles), potential_ligand_sequences
)
logger.error(message)
results = pd.DataFrame()
os.remove(outtmp)
return results
def mhc2_prediction(self, mhc_alleles: List[str],
sequence) -> List[PredictedEpitope]:
""" Performs netmhcIIpan prediction for desired hla alleles and writes result to temporary file."""
# TODO: integrate generate_mhc_ii_alelle_combinations() here to easu utilisation
tmp_fasta = intermediate_files.create_temp_fasta(
[sequence], prefix="tmp_singleseq_")
tmp_folder = tempfile.mkdtemp(prefix="tmp_netmhcIIpan_")
lines, _ = self.runner.run_command([
self.configuration.net_mhc2_pan,
"-BA",
"-a",
",".join(mhc_alleles),
"-f",
tmp_fasta,
"-tdir",
tmp_folder,
"-dirty",
])
return self._parse_netmhcpan_output(lines)
def mhc_prediction(self, mhc_alleles: List[Mhc1], set_available_mhc: Set,
sequence) -> List[PredictedEpitope]:
"""Performs netmhcpan4 prediction for desired hla allele and writes result to temporary file."""
input_fasta = intermediate_files.create_temp_fasta(
sequences=[sequence], prefix="tmp_singleseq_")
available_alleles = self._get_only_available_alleles(
mhc_alleles, set_available_mhc)
if available_alleles is None or available_alleles == "":
raise NeofoxCommandException(
"None of the provided MHC I alleles are supported: {}".format(
mhc_alleles))
cmd = [
self.configuration.net_mhc_pan,
"-a",
available_alleles,
"-f",
input_fasta,
"-BA",
]
lines, _ = self.runner.run_command(cmd)
return self._parse_netmhcpan_output(lines)