def predict_mhci_binding(job, peptfile, allele, peplen, univ_options, mhci_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhci binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param str peplen: Length of peptides to process
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhci_options: Options specific to mhci binding prediction
:return: fsID for file containing the predictions
:rtype: toil.fileStore.FileID
"""
job.fileStore.logToMaster('Running mhci on %s:%s:%s' % (univ_options['patient'], allele,
peplen))
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile())
parameters = [mhci_options['pred'],
allele,
peplen,
input_files['peptfile.faa']]
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhci', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhci_options['version'])
output_file = job.fileStore.writeGlobalFile(predfile.name)
return output_file
def predict_mhcii_binding(job, peptfile, allele, univ_options, mhcii_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhcii binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhcii_options: Options specific to mhcii binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used
:rtype: tuple(toil.fileStore.FileID, str|None)
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
parameters = [mhcii_options['pred'],
allele,
input_files['peptfile.faa']]
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile()), None
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhcii', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhcii_options['version'])
run_netmhciipan = True
predictor = None
with open(predfile.name, 'r') as predfile:
for line in predfile:
if not line.startswith('HLA'):
continue
if line.strip().split('\t')[5] == 'NetMHCIIpan':
break
# If the predictor type is sturniolo then it needs to be processed differently
elif line.strip().split('\t')[5] == 'Sturniolo':
predictor = 'Sturniolo'
else:
predictor = 'Consensus'
run_netmhciipan = False
break
if run_netmhciipan:
netmhciipan = job.addChildJobFn(predict_netmhcii_binding, peptfile, allele, univ_options,
mhcii_options['netmhciipan'], disk='100M', memory='100M',
cores=1)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return netmhciipan.rv()
else:
output_file = job.fileStore.writeGlobalFile(predfile.name)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return output_file, predictor
def predict_netmhcii_binding(job, peptfile, allele, univ_options,
netmhciipan_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using netMHCIIpan.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict netmhciipan_options: Options specific to netmhciipan binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used (netMHCIIpan)
:rtype: tuple(toil.fileStore.FileID, str)
"""
work_dir = os.getcwd()
input_files = {'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job,
input_files,
work_dir,
docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(
job.fileStore.getLocalTempFile()), None
# netMHCIIpan accepts differently formatted alleles so we need to modify the input alleles
if allele.startswith('HLA-DQA') or allele.startswith('HLA-DPA'):
allele = re.sub(r'[*:]', '', allele)
allele = re.sub(r'/', '-', allele)
elif allele.startswith('HLA-DRB'):
allele = re.sub(r':', '', allele)
allele = re.sub(r'\*', '_', allele)
allele = allele.lstrip('HLA-')
else:
raise RuntimeError('Unknown allele seen')
parameters = [
'-a', allele, '-xls', '1', '-xlsfile', 'predictions.tsv', '-f',
input_files['peptfile.faa']
]
# netMHC writes a lot of useless stuff to sys.stdout so we open /dev/null and dump output there.
with open(os.devnull, 'w') as output_catcher:
docker_call(tool='netmhciipan',
tool_parameters=parameters,
work_dir=work_dir,
dockerhub=univ_options['dockerhub'],
outfile=output_catcher,
tool_version=netmhciipan_options['version'])
output_file = job.fileStore.writeGlobalFile('/'.join(
[work_dir, 'predictions.tsv']))
job.fileStore.logToMaster('Ran netmhciipan on %s successfully' % allele)
return output_file, 'netMHCIIpan'
def merge_mhc_peptide_calls(job, antigen_predictions, transgened_files,
univ_options):
"""
Merge all the calls generated by spawn_antigen_predictors.
:param dict antigen_predictions: The return value from running :meth:`spawn_antigen_predictors`
:param dict transgened_files: The transgened peptide files
:param dict univ_options: Universal options for ProTECT
:return: merged binding predictions
output_files:
|- 'mhcii_merged_files.list': fsID
+- 'mhci_merged_files.list': fsID
:rtype: dict
"""
job.fileStore.logToMaster('Merging MHC calls')
work_dir = os.getcwd()
pept_files = {
'10_mer.faa':
transgened_files['transgened_tumor_10_mer_snpeffed.faa'],
'10_mer.faa.map':
transgened_files['transgened_tumor_10_mer_snpeffed.faa.map'],
'15_mer.faa':
transgened_files['transgened_tumor_15_mer_snpeffed.faa'],
'15_mer.faa.map':
transgened_files['transgened_tumor_15_mer_snpeffed.faa.map']
}
pept_files = get_files_from_filestore(job, pept_files, work_dir)
mhci_preds, mhcii_preds = antigen_predictions
mhci_called = mhcii_called = False
# Merge MHCI calls
# Read 10-mer pepts into memory
peptides = read_peptide_file(pept_files['10_mer.faa'])
with open(pept_files['10_mer.faa.map'], 'r') as mapfile:
pepmap = json.load(mapfile)
with open('/'.join([work_dir, 'mhci_merged_files.list']),
'w') as mhci_resfile:
for key in mhci_preds:
tumor_file = job.fileStore.readGlobalFile(mhci_preds[key]['tumor'])
with open(tumor_file) as t_f:
tumor_df = pandas.read_json(eval(t_f.read()))
if tumor_df.empty:
continue
mhci_called = True
# TODO: There must be a better way of doing this
normal_df = _process_mhci(job.fileStore.readGlobalFile(
mhci_preds[key]['normal']),
normal=True)
normal_dict = normal_df.set_index('pept')['tumor_pred']
normal_preds = [
normal_dict[x] for x in list(tumor_df['normal_pept'])
]
tumor_df['normal_pred'] = normal_preds
for pred in tumor_df.itertuples():
print_mhc_peptide(pred, peptides, pepmap, mhci_resfile)
# Merge MHCII calls
# read 15-mer pepts into memory
peptides = read_peptide_file(pept_files['15_mer.faa'])
with open(pept_files['15_mer.faa.map'], 'r') as mapfile:
pepmap = json.load(mapfile)
# Incorporate peptide names into the merged calls
with open('/'.join([work_dir, 'mhcii_merged_files.list']), 'w') as \
mhcii_resfile:
for key in mhcii_preds:
if mhcii_preds[key]['predictor'] is None:
continue
mhcii_called = True
tumor_file = job.fileStore.readGlobalFile(
mhcii_preds[key]['tumor'])
with open(tumor_file) as t_f:
tumor_df = pandas.read_json(eval(t_f.read()))
if tumor_df.empty:
continue
# TODO: There must be a better way of doing this
if mhcii_preds[key]['predictor'] == 'Consensus':
normal_df = _process_consensus_mhcii(
job.fileStore.readGlobalFile(
mhcii_preds[key]['normal'][0]),
normal=True)
elif mhcii_preds[key]['predictor'] == 'Sturniolo':
normal_df = _process_sturniolo_mhcii(
job.fileStore.readGlobalFile(
mhcii_preds[key]['normal'][0]),
normal=True)
elif mhcii_preds[key]['predictor'] == 'netMHCIIpan':
normal_df = _process_net_mhcii(job.fileStore.readGlobalFile(
mhcii_preds[key]['normal'][0]),
normal=True)
else:
assert False
normal_dict = normal_df.set_index('pept')['tumor_pred']
normal_preds = [
normal_dict[x] for x in list(tumor_df['normal_pept'])
]
tumor_df['normal_pred'] = normal_preds
for pred in tumor_df.itertuples():
print_mhc_peptide(
pred,
peptides,
pepmap,
mhcii_resfile,
netmhc=mhcii_preds[key]['predictor'] == 'netMHCIIpan')
if not (mhci_called or mhcii_called):
raise RuntimeError('No peptides available for ranking')
output_files = defaultdict()
for mhc_file in [mhci_resfile.name, mhcii_resfile.name]:
output_files[os.path.split(mhc_file)
[1]] = job.fileStore.writeGlobalFile(mhc_file)
export_results(job,
output_files[os.path.split(mhc_file)[1]],
mhc_file,
univ_options,
subfolder='binding_predictions')
return output_files