def parse_outputs(self, chunks):
split_parsed_output_files = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
if self.input_file_type == 'fasta':
fasta_chunk = tsv_chunk
else:
fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
for a in self.alleles:
for epl in self.epitope_lengths:
split_iedb_output_files = []
status_message("Parsing binding predictions for Allele %s and Epitope Length %s - Entries %s" % (a, epl, fasta_chunk))
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
if hasattr(prediction, 'iedb_prediction_method'):
iedb_method = prediction.iedb_prediction_method
else:
iedb_method = method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
continue
valid_lengths = prediction.valid_lengths_for_allele(a)
if epl not in valid_lengths:
continue
split_iedb_out = os.path.join(self.tmp_dir, ".".join([self.sample_name, iedb_method, a, str(epl), "tsv_%s" % fasta_chunk]))
if os.path.exists(split_iedb_out):
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(self.tmp_dir, ".".join([self.sample_name, a, str(epl), "parsed", "tsv_%s" % fasta_chunk]))
if os.path.exists(split_parsed_file_path):
status_message("Parsed Output File for Allele %s and Epitope Length %s (Entries %s) already exists. Skipping" % (a, epl, fasta_chunk))
split_parsed_output_files.append(split_parsed_file_path)
continue
if self.input_file_type == 'pvacvector_input_fasta':
split_fasta_file_path = "{}_1-2.{}.tsv".format(self.split_fasta_basename(), epl)
else:
split_fasta_file_path = "%s_%s"%(self.split_fasta_basename(), fasta_chunk)
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message("Parsing prediction file for Allele %s and Epitope Length %s - Entries %s" % (a, epl, fasta_chunk))
split_tsv_file_path = "%s_%s" % (self.tsv_file_path(), tsv_chunk)
params = {
'input_iedb_files' : split_iedb_output_files,
'input_tsv_file' : split_tsv_file_path,
'key_file' : split_fasta_key_file_path,
'output_file' : split_parsed_file_path,
}
if self.additional_report_columns and 'sample_name' in self.additional_report_columns:
params['sample_name'] = self.sample_name
else:
params['sample_name'] = None
parser = self.output_parser(params)
parser.execute()
status_message("Parsing prediction file for Allele %s and Epitope Length %s - Entries %s - Completed" % (a, epl, fasta_chunk))
split_parsed_output_files.append(split_parsed_file_path)
return split_parsed_output_files
def call_iedb_and_parse_outputs(self, chunks):
split_parsed_output_files = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
for a in self.alleles:
split_fasta_file_path = "%s_%s"%(self.split_fasta_basename(), fasta_chunk)
split_iedb_output_files = []
status_message("Processing entries for Allele %s - Entries %s" % (a, fasta_chunk))
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
iedb_method = prediction.iedb_prediction_method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
status_message("Allele %s not valid for Method %s. Skipping." % (a, method))
continue
split_iedb_out = os.path.join(self.tmp_dir, ".".join([self.sample_name, iedb_method, a, "tsv_%s" % fasta_chunk]))
if os.path.exists(split_iedb_out):
status_message("IEDB file for Allele %s with Method %s (Entries %s) already exists. Skipping." % (a, method, fasta_chunk))
split_iedb_output_files.append(split_iedb_out)
continue
status_message("Running IEDB on Allele %s with Method %s - Entries %s" % (a, method, fasta_chunk))
lib.call_iedb.main([
split_fasta_file_path,
split_iedb_out,
iedb_method,
a,
'-r', str(self.iedb_retries),
'-e', self.iedb_executable,
])
status_message("Completed")
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(self.tmp_dir, ".".join([self.sample_name, a, "parsed", "tsv_%s" % fasta_chunk]))
if os.path.exists(split_parsed_file_path):
status_message("Parsed Output File for Allele %s (Entries %s) already exists. Skipping" % (a, fasta_chunk))
split_parsed_output_files.append(split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message("Parsing IEDB Output for Allele %s - Entries %s" % (a, fasta_chunk))
split_tsv_file_path = "%s_%s" % (self.tsv_file_path(), tsv_chunk)
params = [
*split_iedb_output_files,
split_tsv_file_path,
split_fasta_key_file_path,
split_parsed_file_path,
'-m', self.top_score_metric,
]
if self.top_result_per_mutation == True:
params.append('-t')
lib.parse_output.main(params)
status_message("Completed")
split_parsed_output_files.append(split_parsed_file_path)
return split_parsed_output_files
def valid_alleles_per_algorithm(prediction_algorithms):
valid_allele_list = {}
for algorithm in prediction_algorithms.split(","):
prediction_class = globals()[algorithm]
alleles = prediction_class().valid_allele_names()
# alleles sometimes returns as dict_keys instead of an array, so must specify as list
valid_allele_list[algorithm] = list(alleles)
return valid_allele_list
def valid_alleles(prediction_algorithms):
valid_allele_list = {}
for algorithm in prediction_algorithms.split(","):
prediction_class = globals()[algorithm]
alleles = prediction_class().valid_allele_names()
# alleles sometimes returns as dict_keys instead of an array, so must specify as list
valid_allele_list[algorithm] = list(alleles)
return valid_allele_list
def main(args_input = sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
if args.prediction_algorithm is None:
print('\n'.join(sorted(PredictionClass.all_valid_allele_names())))
else:
prediction_class = globals()[args.prediction_algorithm]
print("\n".join(sorted(prediction_class().valid_allele_names())))
def main(args_input=sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
if args.prediction_algorithm is None:
print('\n'.join(sorted(PredictionClass.all_valid_allele_names())))
else:
prediction_class = globals()[args.prediction_algorithm]
print("\n".join(sorted(prediction_class().valid_allele_names())))
def main(args_input=sys.argv[1:]):
parser = argparse.ArgumentParser(
'pvacseq call_iedb',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input_file',
type=argparse.FileType('r'),
help="Input FASTA file")
parser.add_argument('output_file', help="Output file from iedb")
parser.add_argument('method',
choices=PredictionClass.prediction_methods(),
help="The iedb analysis method to use")
parser.add_argument('allele', help="Allele for which to make prediction")
parser.add_argument('-l',
'--epitope-length',
type=int,
choices=[8, 9, 10, 11, 12, 13, 14, 15],
help="Length of subpeptides (epitopes) to predict")
parser.add_argument(
"-r",
"--iedb-retries",
type=int,
default=5,
help=
"Number of retries when making requests to the IEDB RESTful web interface. Must be less than or equal to 100."
)
parser.add_argument("-e",
"--iedb-executable-path",
help="The executable path of the local IEDB install")
args = parser.parse_args(args_input)
PredictionClass.check_alleles_valid([args.allele])
prediction_class = getattr(sys.modules[__name__], args.method)
prediction_class_object = prediction_class()
prediction_class_object.check_allele_valid(args.allele)
prediction_class_object.check_length_valid_for_allele(
args.epitope_length, args.allele)
if args.epitope_length is None and prediction_class_object.needs_epitope_length:
sys.exit("Epitope length is required for class I binding predictions")
(response_text, output_mode) = prediction_class_object.predict(
args.input_file, args.allele, args.epitope_length,
args.iedb_executable_path, args.iedb_retries)
tmp_output_file = args.output_file + '.tmp'
if output_mode == 'pandas':
response_text.to_csv(tmp_output_file, index=False, sep="\t")
else:
tmp_output_filehandle = open(tmp_output_file, output_mode)
tmp_output_filehandle.write(response_text)
tmp_output_filehandle.close()
os.replace(tmp_output_file, args.output_file)
args.input_file.close()
def main(args_input=sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
if "." in args.sample_name:
sys.exit("Sample name cannot contain '.'")
if args.fasta_size % 2 != 0:
sys.exit("The fasta size needs to be an even number")
if args.iedb_retries > 100:
sys.exit(
"The number of IEDB retries must be less than or equal to 100")
if args.downstream_sequence_length == 'full':
downstream_sequence_length = None
elif args.downstream_sequence_length.isdigit():
downstream_sequence_length = int(args.downstream_sequence_length)
else:
sys.exit(
"The downstream sequence length needs to be a positive integer or 'full'"
)
# if args.iedb_install_directory:
# lib.call_iedb.setup_iedb_conda_env()
input_file_type = 'bedpe'
base_output_dir = os.path.abspath(args.output_dir)
class_i_prediction_algorithms = []
class_ii_prediction_algorithms = []
for prediction_algorithm in sorted(args.prediction_algorithms):
prediction_class = globals()[prediction_algorithm]
prediction_class_object = prediction_class()
if isinstance(prediction_class_object, MHCI):
class_i_prediction_algorithms.append(prediction_algorithm)
elif isinstance(prediction_class_object, MHCII):
class_ii_prediction_algorithms.append(prediction_algorithm)
class_i_alleles = []
class_ii_alleles = []
for allele in sorted(set(args.allele)):
valid = 0
if allele in MHCI.all_valid_allele_names():
class_i_alleles.append(allele)
valid = 1
if allele in MHCII.all_valid_allele_names():
class_ii_alleles.append(allele)
valid = 1
if not valid:
print("Allele %s not valid. Skipping." % allele)
shared_arguments = {
'input_file': args.input_file,
'input_file_type': input_file_type,
'sample_name': args.sample_name,
'top_score_metric': args.top_score_metric,
'binding_threshold': args.binding_threshold,
'allele_specific_cutoffs': args.allele_specific_binding_thresholds,
'net_chop_method': args.net_chop_method,
'net_chop_threshold': args.net_chop_threshold,
'additional_report_columns': args.additional_report_columns,
'fasta_size': args.fasta_size,
'iedb_retries': args.iedb_retries,
'downstream_sequence_length': downstream_sequence_length,
'keep_tmp_files': args.keep_tmp_files,
'n_threads': args.n_threads,
}
if len(class_i_prediction_algorithms) > 0 and len(class_i_alleles) > 0:
if args.epitope_length is None:
sys.exit(
"Epitope length is required for class I binding predictions")
if args.iedb_install_directory:
iedb_mhc_i_executable = os.path.join(args.iedb_install_directory,
'mhc_i', 'src',
'predict_binding.py')
if not os.path.exists(iedb_mhc_i_executable):
sys.exit("IEDB MHC I executable path doesn't exist %s" %
iedb_mhc_i_executable)
else:
iedb_mhc_i_executable = None
print("Executing MHC Class I predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_I')
os.makedirs(output_dir, exist_ok=True)
class_i_arguments = shared_arguments.copy()
class_i_arguments['alleles'] = class_i_alleles
class_i_arguments[
'peptide_sequence_length'] = args.peptide_sequence_length
class_i_arguments['iedb_executable'] = iedb_mhc_i_executable
class_i_arguments['epitope_lengths'] = args.epitope_length
class_i_arguments[
'prediction_algorithms'] = class_i_prediction_algorithms
class_i_arguments['output_dir'] = output_dir
class_i_arguments['netmhc_stab'] = args.netmhc_stab
pipeline = Pipeline(**class_i_arguments)
pipeline.execute()
elif len(class_i_prediction_algorithms) == 0:
print(
"No MHC class I prediction algorithms chosen. Skipping MHC class I predictions."
)
elif len(class_i_alleles) == 0:
print(
"No MHC class I alleles chosen. Skipping MHC class I predictions.")
if len(class_ii_prediction_algorithms) > 0 and len(class_ii_alleles) > 0:
if args.iedb_install_directory:
iedb_mhc_ii_executable = os.path.join(args.iedb_install_directory,
'mhc_ii',
'mhc_II_binding.py')
if not os.path.exists(iedb_mhc_ii_executable):
sys.exit("IEDB MHC II executable path doesn't exist %s" %
iedb_mhc_ii_executable)
else:
iedb_mhc_ii_executable = None
print("Executing MHC Class II predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_II')
os.makedirs(output_dir, exist_ok=True)
class_ii_arguments = shared_arguments.copy()
class_ii_arguments['alleles'] = class_ii_alleles
class_ii_arguments[
'prediction_algorithms'] = class_ii_prediction_algorithms
class_ii_arguments['peptide_sequence_length'] = 31
class_ii_arguments['iedb_executable'] = iedb_mhc_ii_executable
class_ii_arguments['epitope_lengths'] = [15]
class_ii_arguments['output_dir'] = output_dir
class_ii_arguments['netmhc_stab'] = False
pipeline = Pipeline(**class_ii_arguments)
pipeline.execute()
elif len(class_ii_prediction_algorithms) == 0:
print(
"No MHC class II prediction algorithms chosen. Skipping MHC class II predictions."
)
elif len(class_ii_alleles) == 0:
print(
"No MHC class II alleles chosen. Skipping MHC class II predictions."
)
if len(class_i_prediction_algorithms) > 0 and len(
class_i_alleles) > 0 and len(class_ii_prediction_algorithms
) > 0 and len(class_ii_alleles) > 0:
print("Creating combined reports")
create_combined_reports(base_output_dir, args)
def call_iedb_and_parse_outputs(self, chunks):
split_parsed_output_files = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
for a in self.alleles:
split_fasta_file_path = "%s_%s"%(self.split_fasta_basename(), fasta_chunk)
split_iedb_output_files = []
status_message("Processing entries for Allele %s - Entries %s" % (a, fasta_chunk))
if os.path.getsize(split_fasta_file_path) == 0:
status_message("Fasta file is empty. Skipping")
continue
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
if hasattr(prediction, 'iedb_prediction_method'):
iedb_method = prediction.iedb_prediction_method
else:
iedb_method = method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
status_message("Allele %s not valid for Method %s. Skipping." % (a, method))
continue
split_iedb_out = os.path.join(self.tmp_dir, ".".join([self.sample_name, iedb_method, a, "tsv_%s" % fasta_chunk]))
if os.path.exists(split_iedb_out):
status_message("IEDB file for Allele %s with Method %s (Entries %s) already exists. Skipping." % (a, method, fasta_chunk))
split_iedb_output_files.append(split_iedb_out)
continue
status_message("Running IEDB on Allele %s with Method %s - Entries %s" % (a, method, fasta_chunk))
if not os.environ.get('TEST_FLAG') or os.environ.get('TEST_FLAG') == '0':
if 'last_execute_timestamp' in locals() and not self.iedb_executable:
elapsed_time = ( datetime.datetime.now() - last_execute_timestamp ).total_seconds()
wait_time = 60 - elapsed_time
if wait_time > 0:
time.sleep(wait_time)
lib.call_iedb.main([
split_fasta_file_path,
split_iedb_out,
method,
a,
'-r', str(self.iedb_retries),
'-e', self.iedb_executable,
])
last_execute_timestamp = datetime.datetime.now()
status_message("Completed")
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(self.tmp_dir, ".".join([self.sample_name, a, "parsed", "tsv_%s" % fasta_chunk]))
if os.path.exists(split_parsed_file_path):
status_message("Parsed Output File for Allele %s (Entries %s) already exists. Skipping" % (a, fasta_chunk))
split_parsed_output_files.append(split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message("Parsing IEDB Output for Allele %s - Entries %s" % (a, fasta_chunk))
split_tsv_file_path = "%s_%s" % (self.tsv_file_path(), tsv_chunk)
params = {
'input_iedb_files' : split_iedb_output_files,
'input_tsv_file' : split_tsv_file_path,
'key_file' : split_fasta_key_file_path,
'output_file' : split_parsed_file_path,
}
if self.additional_report_columns and 'sample_name' in self.additional_report_columns:
params['sample_name'] = self.sample_name
else:
params['sample_name'] = None
parser = self.output_parser(params)
parser.execute()
status_message("Completed")
split_parsed_output_files.append(split_parsed_file_path)
return split_parsed_output_files
def call_iedb_and_parse_outputs(self, chunks):
split_parsed_output_files = []
for chunk in chunks:
for a in self.alleles:
split_fasta_file_path = "%s_%s" % (self.split_fasta_basename(),
chunk)
split_iedb_output_files = []
print("Processing entries for Allele %s - Entries %s" %
(a, chunk))
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
iedb_method = prediction.iedb_prediction_method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
print("Allele %s not valid for Method %s. Skipping." %
(a, method))
continue
split_iedb_out = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, iedb_method, a,
"tsv_%s" % chunk
]))
if os.path.exists(split_iedb_out):
print(
"IEDB file for Allele %s with Method %s (Entries %s) already exists. Skipping."
% (a, method, chunk))
split_iedb_output_files.append(split_iedb_out)
continue
print(
"Running IEDB on Allele %s with Method %s - Entries %s"
% (a, method, chunk))
lib.call_iedb.main([
split_fasta_file_path,
split_iedb_out,
iedb_method,
a,
])
print("Completed")
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(
self.tmp_dir,
".".join([self.sample_name, a, "parsed",
"tsv_%s" % chunk]))
if os.path.exists(split_parsed_file_path):
print(
"Parsed Output File for Allele %s (Entries %s) already exists. Skipping"
% (a, chunk))
split_parsed_output_files.append(split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
print("Parsing IEDB Output for Allele %s - Entries %s" %
(a, chunk))
params = [
*split_iedb_output_files,
self.tsv_file_path(),
split_fasta_key_file_path,
split_parsed_file_path,
'-m',
self.top_score_metric,
]
if self.top_result_per_mutation == True:
params.append('-t')
lib.parse_output.main(params)
print("Completed")
split_parsed_output_files.append(split_parsed_file_path)
return split_parsed_output_files
def call_iedb_and_parse_outputs(self, chunks):
split_parsed_output_files = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
fasta_chunk = "%d-%d" % (split_start*2-1, split_end*2)
for a in self.alleles:
for epl in self.epitope_lengths:
split_fasta_file_path = "%s_%s"%(self.split_fasta_basename(), fasta_chunk)
split_iedb_output_files = []
status_message("Processing entries for Allele %s and Epitope Length %s - Entries %s" % (a, epl, fasta_chunk))
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
iedb_method = prediction.iedb_prediction_method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
status_message("Allele %s not valid for Method %s. Skipping." % (a, method))
continue
valid_lengths = prediction.valid_lengths_for_allele(a)
if epl not in valid_lengths:
status_message("Epitope Length %s is not valid for Method %s and Allele %s. Skipping." % (epl, method, a))
continue
split_iedb_out = os.path.join(self.tmp_dir, ".".join([self.sample_name, iedb_method, a, str(epl), "tsv_%s" % fasta_chunk]))
if os.path.exists(split_iedb_out):
status_message("IEDB file for Allele %s and Epitope Length %s with Method %s (Entries %s) already exists. Skipping." % (a, epl, method, fasta_chunk))
split_iedb_output_files.append(split_iedb_out)
continue
status_message("Running IEDB on Allele %s and Epitope Length %s with Method %s - Entries %s" % (a, epl, method, fasta_chunk))
if not os.environ.get('TEST_FLAG') or os.environ.get('TEST_FLAG') == '0':
if 'last_execute_timestamp' in locals() and not self.iedb_executable:
elapsed_time = ( datetime.datetime.now() - last_execute_timestamp ).total_seconds()
wait_time = 60 - elapsed_time
if wait_time > 0:
time.sleep(wait_time)
lib.call_iedb.main([
split_fasta_file_path,
split_iedb_out,
iedb_method,
a,
'-l', str(epl),
'-r', str(self.iedb_retries),
'-e', self.iedb_executable,
])
last_execute_timestamp = datetime.datetime.now()
status_message("Completed")
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(self.tmp_dir, ".".join([self.sample_name, a, str(epl), "parsed", "tsv_%s" % fasta_chunk]))
if os.path.exists(split_parsed_file_path):
status_message("Parsed Output File for Allele %s and Epitope Length %s (Entries %s) already exists. Skipping" % (a, epl, fasta_chunk))
split_parsed_output_files.append(split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message("Parsing IEDB Output for Allele %s and Epitope Length %s - Entries %s" % (a, epl, fasta_chunk))
split_tsv_file_path = "%s_%s" % (self.tsv_file_path(), tsv_chunk)
params = [
*split_iedb_output_files,
split_tsv_file_path,
split_fasta_key_file_path,
split_parsed_file_path,
'-m', self.top_score_metric,
]
if self.top_result_per_mutation == True:
params.append('-t')
lib.parse_output.main(params)
status_message("Completed")
split_parsed_output_files.append(split_parsed_file_path)
return split_parsed_output_files
def call_iedb(self, chunks, length):
alleles = self.alleles
prediction_algorithms = self.prediction_algorithms
argument_sets = []
warning_messages = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
if self.input_file_type == 'fasta':
fasta_chunk = tsv_chunk
else:
fasta_chunk = "%d-%d" % (split_start * 2 - 1, split_end * 2)
for a in alleles:
split_fasta_file_path = "%s_%s" % (
self.split_fasta_basename(length), fasta_chunk)
if os.path.getsize(split_fasta_file_path) == 0:
msg = "Fasta file {} is empty. Skipping".format(
split_fasta_file_path)
if msg not in warning_messages:
warning_messages.append(msg)
continue
#begin of per-algorithm processing
for method in prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
if hasattr(prediction, 'iedb_prediction_method'):
iedb_method = prediction.iedb_prediction_method
else:
iedb_method = method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
msg = "Allele %s not valid for Method %s. Skipping." % (
a, method)
if msg not in warning_messages:
warning_messages.append(msg)
continue
valid_lengths = prediction.valid_lengths_for_allele(a)
if length not in valid_lengths:
msg = "Epitope Length %s is not valid for Method %s and Allele %s. Skipping." % (
length, method, a)
if msg not in warning_messages:
warning_messages.append(msg)
continue
split_iedb_out = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, iedb_method, a,
str(length),
"tsv_%s" % fasta_chunk
]))
if os.path.exists(split_iedb_out):
msg = "Prediction file for Allele %s and Epitope Length %s with Method %s (Entries %s) already exists. Skipping." % (
a, length, method, fasta_chunk)
if msg not in warning_messages:
warning_messages.append(msg)
continue
arguments = [
split_fasta_file_path,
split_iedb_out,
method,
a,
'-r',
str(self.iedb_retries),
'-e',
self.iedb_executable,
]
if not isinstance(prediction, IEDBMHCII):
arguments.extend([
'-l',
str(length),
])
argument_sets.append(arguments)
for msg in warning_messages:
status_message(msg)
with pymp.Parallel(self.n_threads) as p:
for index in p.range(len(argument_sets)):
arguments = argument_sets[index]
a = arguments[3]
method = arguments[2]
filename = arguments[1]
if len(arguments) == 10:
epl = arguments[9]
else:
epl = 15
p.print(
"Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s"
% (a, epl, method, filename))
lib.call_iedb.main(arguments)
p.print(
"Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed"
% (a, epl, method, filename))
def call_iedb_and_parse_outputs(self, chunks):
pymp.config.nested = True
alleles = self.alleles
epitope_lengths = self.epitope_lengths
prediction_algorithms = self.prediction_algorithms
iteration_info = {
'file': {
'total_iterations': len(chunks),
'iterations_per_thread': len(chunks),
'threads': 1,
},
'allele': {
'total_iterations': len(alleles),
'iterations_per_thread': len(alleles),
'threads': 1,
},
'length': {
'total_iterations': len(epitope_lengths),
'iterations_per_thread': len(epitope_lengths),
'threads': 1,
},
'algorithm': {
'total_iterations': len(prediction_algorithms),
'iterations_per_thread': len(prediction_algorithms),
'threads': 1,
},
}
iteration_info = self.balance_multithreads(iteration_info)
split_parsed_output_files = []
lock = Lock()
with pymp.Parallel(iteration_info['file']['threads']) as p:
for i in p.range(len(chunks)):
(split_start, split_end) = chunks[i]
tsv_chunk = "%d-%d" % (split_start, split_end)
fasta_chunk = "%d-%d" % (split_start * 2 - 1, split_end * 2)
with pymp.Parallel(iteration_info['allele']['threads']) as p2:
for j in p2.range(len(alleles)):
a = alleles[j]
with pymp.Parallel(
iteration_info['length']['threads']) as p3:
for k in p3.range(len(epitope_lengths)):
epl = epitope_lengths[k]
if self.input_file_type == 'pvacvector_input_fasta':
split_fasta_file_path = "{}_1-2.{}.tsv".format(
self.split_fasta_basename(), epl)
else:
split_fasta_file_path = "%s_%s" % (
self.split_fasta_basename(),
fasta_chunk)
split_iedb_output_files = []
status_message_with_lock(
"Processing entries for Allele %s and Epitope Length %s - Entries %s"
% (a, epl, fasta_chunk), lock)
if os.path.getsize(split_fasta_file_path) == 0:
status_message_with_lock(
"Fasta file is empty. Skipping", lock)
continue
#begin of per-algorithm processing
with pymp.Parallel(iteration_info['algorithm']
['threads']) as p4:
for m in p4.range(
len(prediction_algorithms)):
method = prediction_algorithms[m]
prediction_class = globals()[method]
prediction = prediction_class()
if hasattr(prediction,
'iedb_prediction_method'):
iedb_method = prediction.iedb_prediction_method
else:
iedb_method = method
valid_alleles = prediction.valid_allele_names(
)
if a not in valid_alleles:
status_message_with_lock(
"Allele %s not valid for Method %s. Skipping."
% (a, method), lock)
continue
valid_lengths = prediction.valid_lengths_for_allele(
a)
if epl not in valid_lengths:
status_message_with_lock(
"Epitope Length %s is not valid for Method %s and Allele %s. Skipping."
% (epl, method, a), lock)
continue
split_iedb_out = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, iedb_method,
a,
str(epl),
"tsv_%s" % fasta_chunk
]))
if os.path.exists(split_iedb_out):
status_message_with_lock(
"IEDB file for Allele %s and Epitope Length %s with Method %s (Entries %s) already exists. Skipping."
%
(a, epl, method, fasta_chunk),
lock)
split_iedb_output_files.append(
split_iedb_out)
continue
status_message_with_lock(
"Running IEDB on Allele %s and Epitope Length %s with Method %s - Entries %s"
% (a, epl, method, fasta_chunk),
lock)
if not os.environ.get(
'TEST_FLAG') or os.environ.get(
'TEST_FLAG') == '0':
if 'last_execute_timestamp' in locals(
) and not self.iedb_executable:
elapsed_time = (
datetime.datetime.now() -
last_execute_timestamp
).total_seconds()
wait_time = 60 - elapsed_time
if wait_time > 0:
time.sleep(wait_time)
arguments = [
split_fasta_file_path,
split_iedb_out,
method,
a,
'-r',
str(self.iedb_retries),
'-e',
self.iedb_executable,
]
if not isinstance(
prediction, IEDBMHCII):
arguments.extend([
'-l',
str(epl),
])
lib.call_iedb.main(arguments)
last_execute_timestamp = datetime.datetime.now(
)
status_message_with_lock(
"Running IEDB on Allele %s and Epitope Length %s with Method %s - Entries %s - Completed"
% (a, epl, method, fasta_chunk),
lock)
split_iedb_output_files.append(
split_iedb_out)
#end of per-algorithm processing
#parse all output files for one allele, epitope, and file chunk over all algorithms into one file
split_parsed_file_path = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, a,
str(epl), "parsed",
"tsv_%s" % fasta_chunk
]))
if os.path.exists(split_parsed_file_path):
status_message_with_lock(
"Parsed Output File for Allele %s and Epitope Length %s (Entries %s) already exists. Skipping"
% (a, epl, fasta_chunk), lock)
split_parsed_output_files.append(
split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message_with_lock(
"Parsing IEDB Output for Allele %s and Epitope Length %s - Entries %s"
% (a, epl, fasta_chunk), lock)
split_tsv_file_path = "%s_%s" % (
self.tsv_file_path(), tsv_chunk)
params = {
'input_iedb_files':
split_iedb_output_files,
'input_tsv_file': split_tsv_file_path,
'key_file': split_fasta_key_file_path,
'output_file': split_parsed_file_path,
}
if self.additional_report_columns and 'sample_name' in self.additional_report_columns:
params[
'sample_name'] = self.sample_name
else:
params['sample_name'] = None
parser = self.output_parser(params)
parser.execute()
status_message_with_lock(
"Parsing IEDB Output for Allele %s and Epitope Length %s - Entries %s - Completed"
% (a, epl, fasta_chunk), lock)
split_parsed_output_files.append(
split_parsed_file_path)
return split_parsed_output_files
def main(args_input=sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
PredictionClass.check_alleles_valid(args.allele)
if "." in args.sample_name:
sys.exit("Sample name cannot contain '.'")
if args.fasta_size % 2 != 0:
sys.exit("The fasta size needs to be an even number")
if args.downstream_sequence_length == 'full':
downstream_sequence_length = None
elif args.downstream_sequence_length.isdigit():
downstream_sequence_length = args.downstream_sequence_length
else:
sys.exit(
"The downstream sequence length needs to be a positive integer or 'full'"
)
base_output_dir = os.path.abspath(args.output_dir)
class_i_prediction_algorithms = []
class_ii_prediction_algorithms = []
for prediction_algorithm in args.prediction_algorithms:
prediction_class = globals()[prediction_algorithm]
prediction_class_object = prediction_class()
if isinstance(prediction_class_object, MHCI):
class_i_prediction_algorithms.append(prediction_algorithm)
elif isinstance(prediction_class_object, MHCII):
class_ii_prediction_algorithms.append(prediction_algorithm)
shared_arguments = {
'input_file': args.input_file,
'sample_name': args.sample_name,
'alleles': args.allele,
'top_result_per_mutation': args.top_result_per_mutation,
'top_score_metric': args.top_score_metric,
'binding_threshold': args.binding_threshold,
'minimum_fold_change': args.minimum_fold_change,
'net_chop_method': args.net_chop_method,
'net_chop_threshold': args.net_chop_threshold,
'normal_cov': args.normal_cov,
'normal_vaf': args.normal_vaf,
'tdna_cov': args.tdna_cov,
'tdna_vaf': args.tdna_vaf,
'trna_cov': args.trna_cov,
'trna_vaf': args.trna_vaf,
'expn_val': args.expn_val,
'fasta_size': args.fasta_size,
'downstream_sequence_length': downstream_sequence_length,
'keep_tmp_files': args.keep_tmp_files,
}
additional_input_files = parse_additional_input_file_list(
args.additional_input_file_list)
shared_arguments.update(additional_input_files)
if len(class_i_prediction_algorithms) > 0:
if args.epitope_length is None:
sys.exit(
"Epitope length is required for class I binding predictions")
print("Executing MHC Class I predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_I')
os.makedirs(output_dir, exist_ok=True)
class_i_arguments = shared_arguments.copy()
class_i_arguments[
'peptide_sequence_length'] = args.peptide_sequence_length
class_i_arguments['epitope_lengths'] = args.epitope_length
class_i_arguments[
'prediction_algorithms'] = class_i_prediction_algorithms
class_i_arguments['output_dir'] = output_dir
class_i_arguments['netmhc_stab'] = args.netmhc_stab
pipeline = MHCIPipeline(**class_i_arguments)
pipeline.execute()
if len(class_ii_prediction_algorithms) > 0:
print("Executing MHC Class II predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_II')
os.makedirs(output_dir, exist_ok=True)
class_ii_arguments = shared_arguments.copy()
class_ii_arguments[
'prediction_algorithms'] = class_ii_prediction_algorithms
class_ii_arguments['output_dir'] = output_dir
class_ii_arguments['netmhc_stab'] = False
pipeline = MHCIIPipeline(**class_ii_arguments)
pipeline.execute()
def print_valid_alleles(self):
if self.prediction_algorithm is None:
print('\n'.join(sorted(PredictionClass.all_valid_allele_names())))
else:
prediction_class = globals()[self.prediction_algorithm]
print("\n".join(sorted(prediction_class().valid_allele_names())))
def main(args_input = sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
PredictionClass.check_alleles_valid(args.allele)
if "." in args.sample_name:
sys.exit("Sample name cannot contain '.'")
if args.fasta_size%2 != 0:
sys.exit("The fasta size needs to be an even number")
if args.iedb_retries > 100:
sys.exit("The number of IEDB retries must be less than or equal to 100")
if args.downstream_sequence_length == 'full':
downstream_sequence_length = None
elif args.downstream_sequence_length.isdigit():
downstream_sequence_length = args.downstream_sequence_length
else:
sys.exit("The downstream sequence length needs to be a positive integer or 'full'")
base_output_dir = os.path.abspath(args.output_dir)
class_i_prediction_algorithms = []
class_ii_prediction_algorithms = []
for prediction_algorithm in sorted(args.prediction_algorithms):
prediction_class = globals()[prediction_algorithm]
prediction_class_object = prediction_class()
if isinstance(prediction_class_object, MHCI):
class_i_prediction_algorithms.append(prediction_algorithm)
elif isinstance(prediction_class_object, MHCII):
class_ii_prediction_algorithms.append(prediction_algorithm)
class_i_alleles = []
class_ii_alleles = []
for allele in sorted(set(args.allele)):
if allele in MHCI.all_valid_allele_names():
class_i_alleles.append(allele)
if allele in MHCII.all_valid_allele_names():
class_ii_alleles.append(allele)
shared_arguments = {
'input_file' : args.input_file,
'sample_name' : args.sample_name,
'top_result_per_mutation' : args.top_result_per_mutation,
'top_score_metric' : args.top_score_metric,
'binding_threshold' : args.binding_threshold,
'minimum_fold_change' : args.minimum_fold_change,
'net_chop_method' : args.net_chop_method,
'net_chop_threshold' : args.net_chop_threshold,
'normal_cov' : args.normal_cov,
'normal_vaf' : args.normal_vaf,
'tdna_cov' : args.tdna_cov,
'tdna_vaf' : args.tdna_vaf,
'trna_cov' : args.trna_cov,
'trna_vaf' : args.trna_vaf,
'expn_val' : args.expn_val,
'fasta_size' : args.fasta_size,
'iedb_retries' : args.iedb_retries,
'downstream_sequence_length': downstream_sequence_length,
'keep_tmp_files' : args.keep_tmp_files,
}
additional_input_files = parse_additional_input_file_list(args.additional_input_file_list)
shared_arguments.update(additional_input_files)
if len(class_i_prediction_algorithms) > 0 and len(class_i_alleles) > 0:
if args.epitope_length is None:
sys.exit("Epitope length is required for class I binding predictions")
if args.iedb_install_directory:
iedb_mhc_i_executable = os.path.join(args.iedb_install_directory, 'mhc_i', 'src', 'predict_binding.py')
if not os.path.exists(iedb_mhc_i_executable):
sys.exit("IEDB MHC I executable path doesn't exist %s" % iedb_mhc_i_executable)
else:
iedb_mhc_i_executable = None
print("Executing MHC Class I predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_I')
os.makedirs(output_dir, exist_ok=True)
class_i_arguments = shared_arguments.copy()
class_i_arguments['alleles'] = class_i_alleles
class_i_arguments['peptide_sequence_length'] = args.peptide_sequence_length
class_i_arguments['iedb_executable'] = iedb_mhc_i_executable
class_i_arguments['epitope_lengths'] = args.epitope_length
class_i_arguments['prediction_algorithms'] = class_i_prediction_algorithms
class_i_arguments['output_dir'] = output_dir
class_i_arguments['netmhc_stab'] = args.netmhc_stab
pipeline = MHCIPipeline(**class_i_arguments)
pipeline.execute()
if len(class_ii_prediction_algorithms) > 0 and len(class_ii_alleles) > 0:
if args.iedb_install_directory:
iedb_mhc_ii_executable = os.path.join(args.iedb_install_directory, 'mhc_ii', 'mhc_II_binding.py')
if not os.path.exists(iedb_mhc_ii_executable):
sys.exit("IEDB MHC II executable path doesn't exist %s" % iedb_mhc_ii_executable)
else:
iedb_mhc_ii_executable = None
print("Executing MHC Class II predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_II')
os.makedirs(output_dir, exist_ok=True)
class_ii_arguments = shared_arguments.copy()
class_ii_arguments['alleles'] = class_ii_alleles
class_ii_arguments['prediction_algorithms'] = class_ii_prediction_algorithms
class_ii_arguments['iedb_executable'] = iedb_mhc_ii_executable
class_ii_arguments['output_dir'] = output_dir
class_ii_arguments['netmhc_stab'] = False
pipeline = MHCIIPipeline(**class_ii_arguments)
pipeline.execute()
def main(args_input=sys.argv[1:]):
parser = define_parser()
args = parser.parse_args(args_input)
if args.input_file.endswith('.vcf'):
input_file_type = 'vcf'
elif args.input_file.endswith('.bedpe'):
input_file_type = 'bedpe'
else:
sys.exit(
"Unknown input file type for file (%s). Input file must be either a VCF (.vcf) or a bedpe (.bedpe) file."
% input_file)
if "." in args.sample_name:
sys.exit("Sample name cannot contain '.'")
if args.fasta_size % 2 != 0:
sys.exit("The fasta size needs to be an even number")
if args.iedb_retries > 100:
sys.exit(
"The number of IEDB retries must be less than or equal to 100")
if args.downstream_sequence_length == 'full':
downstream_sequence_length = None
elif args.downstream_sequence_length.isdigit():
downstream_sequence_length = int(args.downstream_sequence_length)
else:
sys.exit(
"The downstream sequence length needs to be a positive integer or 'full'"
)
base_output_dir = os.path.abspath(args.output_dir)
class_i_prediction_algorithms = []
class_ii_prediction_algorithms = []
for prediction_algorithm in sorted(args.prediction_algorithms):
prediction_class = globals()[prediction_algorithm]
prediction_class_object = prediction_class()
if isinstance(prediction_class_object, MHCI):
class_i_prediction_algorithms.append(prediction_algorithm)
elif isinstance(prediction_class_object, MHCII):
class_ii_prediction_algorithms.append(prediction_algorithm)
class_i_alleles = []
class_ii_alleles = []
for allele in sorted(set(args.allele)):
valid = 0
if allele in MHCI.all_valid_allele_names():
class_i_alleles.append(allele)
valid = 1
if allele in MHCII.all_valid_allele_names():
class_ii_alleles.append(allele)
valid = 1
if not valid:
print("Allele %s not valid. Skipping." % allele)
shared_arguments = {
'input_file': args.input_file,
'input_file_type': input_file_type,
'sample_name': args.sample_name,
'top_result_per_mutation': args.top_result_per_mutation,
'top_score_metric': args.top_score_metric,
'binding_threshold': args.binding_threshold,
'minimum_fold_change': args.minimum_fold_change,
'net_chop_method': args.net_chop_method,
'net_chop_threshold': args.net_chop_threshold,
'normal_cov': args.normal_cov,
'normal_vaf': args.normal_vaf,
'tdna_cov': args.tdna_cov,
'tdna_vaf': args.tdna_vaf,
'trna_cov': args.trna_cov,
'trna_vaf': args.trna_vaf,
'expn_val': args.expn_val,
'additional_report_columns': args.additional_report_columns,
'fasta_size': args.fasta_size,
'iedb_retries': args.iedb_retries,
'downstream_sequence_length': downstream_sequence_length,
'keep_tmp_files': args.keep_tmp_files,
}
additional_input_files = parse_additional_input_file_list(
args.additional_input_file_list)
shared_arguments.update(additional_input_files)
if len(class_i_prediction_algorithms) > 0 and len(class_i_alleles) > 0:
if args.epitope_length is None:
sys.exit(
"Epitope length is required for class I binding predictions")
if args.iedb_install_directory:
iedb_mhc_i_executable = os.path.join(args.iedb_install_directory,
'mhc_i', 'src',
'predict_binding.py')
if not os.path.exists(iedb_mhc_i_executable):
sys.exit("IEDB MHC I executable path doesn't exist %s" %
iedb_mhc_i_executable)
else:
iedb_mhc_i_executable = None
print("Executing MHC Class I predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_I')
os.makedirs(output_dir, exist_ok=True)
class_i_arguments = shared_arguments.copy()
class_i_arguments['alleles'] = class_i_alleles
class_i_arguments[
'peptide_sequence_length'] = args.peptide_sequence_length
class_i_arguments['iedb_executable'] = iedb_mhc_i_executable
class_i_arguments['epitope_lengths'] = args.epitope_length
class_i_arguments[
'prediction_algorithms'] = class_i_prediction_algorithms
class_i_arguments['output_dir'] = output_dir
class_i_arguments['netmhc_stab'] = args.netmhc_stab
pipeline = MHCIPipeline(**class_i_arguments)
pipeline.execute()
if len(class_ii_prediction_algorithms) > 0 and len(class_ii_alleles) > 0:
if args.iedb_install_directory:
iedb_mhc_ii_executable = os.path.join(args.iedb_install_directory,
'mhc_ii',
'mhc_II_binding.py')
if not os.path.exists(iedb_mhc_ii_executable):
sys.exit("IEDB MHC II executable path doesn't exist %s" %
iedb_mhc_ii_executable)
else:
iedb_mhc_ii_executable = None
print("Executing MHC Class II predictions")
output_dir = os.path.join(base_output_dir, 'MHC_Class_II')
os.makedirs(output_dir, exist_ok=True)
class_ii_arguments = shared_arguments.copy()
class_ii_arguments['alleles'] = class_ii_alleles
class_ii_arguments[
'prediction_algorithms'] = class_ii_prediction_algorithms
class_ii_arguments['iedb_executable'] = iedb_mhc_ii_executable
class_ii_arguments['output_dir'] = output_dir
class_ii_arguments['netmhc_stab'] = False
pipeline = MHCIIPipeline(**class_ii_arguments)
pipeline.execute()
def call_iedb_and_parse_outputs(self, chunks):
split_parsed_output_files = []
for (split_start, split_end) in chunks:
tsv_chunk = "%d-%d" % (split_start, split_end)
fasta_chunk = "%d-%d" % (split_start * 2 - 1, split_end * 2)
for a in self.alleles:
for epl in self.epitope_lengths:
split_fasta_file_path = "%s_%s" % (
self.split_fasta_basename(), fasta_chunk)
split_iedb_output_files = []
status_message(
"Processing entries for Allele %s and Epitope Length %s - Entries %s"
% (a, epl, fasta_chunk))
for method in self.prediction_algorithms:
prediction_class = globals()[method]
prediction = prediction_class()
iedb_method = prediction.iedb_prediction_method
valid_alleles = prediction.valid_allele_names()
if a not in valid_alleles:
status_message(
"Allele %s not valid for Method %s. Skipping."
% (a, method))
continue
valid_lengths = prediction.valid_lengths_for_allele(a)
if epl not in valid_lengths:
status_message(
"Epitope Length %s is not valid for Method %s and Allele %s. Skipping."
% (epl, method, a))
continue
split_iedb_out = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, iedb_method, a,
str(epl),
"tsv_%s" % fasta_chunk
]))
if os.path.exists(split_iedb_out):
status_message(
"IEDB file for Allele %s and Epitope Length %s with Method %s (Entries %s) already exists. Skipping."
% (a, epl, method, fasta_chunk))
split_iedb_output_files.append(split_iedb_out)
continue
status_message(
"Running IEDB on Allele %s and Epitope Length %s with Method %s - Entries %s"
% (a, epl, method, fasta_chunk))
lib.call_iedb.main([
split_fasta_file_path,
split_iedb_out,
iedb_method,
a,
'-l',
str(epl),
'-r',
str(self.iedb_retries),
'-e',
self.iedb_executable,
])
status_message("Completed")
split_iedb_output_files.append(split_iedb_out)
split_parsed_file_path = os.path.join(
self.tmp_dir, ".".join([
self.sample_name, a,
str(epl), "parsed",
"tsv_%s" % fasta_chunk
]))
if os.path.exists(split_parsed_file_path):
status_message(
"Parsed Output File for Allele %s and Epitope Length %s (Entries %s) already exists. Skipping"
% (a, epl, fasta_chunk))
split_parsed_output_files.append(
split_parsed_file_path)
continue
split_fasta_key_file_path = split_fasta_file_path + '.key'
if len(split_iedb_output_files) > 0:
status_message(
"Parsing IEDB Output for Allele %s and Epitope Length %s - Entries %s"
% (a, epl, fasta_chunk))
split_tsv_file_path = "%s_%s" % (self.tsv_file_path(),
tsv_chunk)
params = [
*split_iedb_output_files,
split_tsv_file_path,
split_fasta_key_file_path,
split_parsed_file_path,
'-m',
self.top_score_metric,
]
if self.top_result_per_mutation == True:
params.append('-t')
lib.parse_output.main(params)
status_message("Completed")
split_parsed_output_files.append(
split_parsed_file_path)
return split_parsed_output_files