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Write IEDB API errors to a log file instead of stdout
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@susannasiebert
susannasiebert committed Jan 17, 2024
1 parent 06d960d commit 159bdcd
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Showing 3 changed files with 38 additions and 19 deletions.
6 changes: 4 additions & 2 deletions pvactools/lib/call_iedb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,16 +30,18 @@ def main(args_input = sys.argv[1:]):
)
parser.add_argument('--tmp-dir',
help="Location to write tmp files to")
parser.add_argument('--log-dir',
help="Location to write log files to")
args = parser.parse_args(args_input)

prediction_class = getattr(sys.modules[__name__], args.method)
prediction_class_object = prediction_class()

try:
(response_text, output_mode) = prediction_class_object.predict(args.input_file, args.allele, args.epitope_length, args.iedb_executable_path, args.iedb_retries, tmp_dir=args.tmp_dir)
(response_text, output_mode) = prediction_class_object.predict(args.input_file, args.allele, args.epitope_length, args.iedb_executable_path, args.iedb_retries, tmp_dir=args.tmp_dir, log_dir=args.log_dir)
except Exception as err:
if str(err) == 'len(peptide_list) != len(scores)':
(response_text, output_mode) = prediction_class_object.predict(args.input_file, args.allele, args.epitope_length, args.iedb_executable_path, args.iedb_retries, tmp_dir=args.tmp_dir)
(response_text, output_mode) = prediction_class_object.predict(args.input_file, args.allele, args.epitope_length, args.iedb_executable_path, args.iedb_retries, tmp_dir=args.tmp_dir, log_dir=args.log_dir)
else:
raise err

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3 changes: 3 additions & 0 deletions pvactools/lib/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -339,6 +339,7 @@ def call_iedb(self, chunks):
'-e', self.iedb_executable,
'-l', str(epl),
'--tmp-dir', self.tmp_dir,
'--log-dir', self.log_dir(),
]
argument_sets.append(arguments)

Expand Down Expand Up @@ -645,6 +646,8 @@ def call_iedb(self, chunks, length):
'-r', str(self.iedb_retries),
'-e', self.iedb_executable,
'-l', str(length),
'--tmp-dir', self.tmp_dir,
'--log-dir', self.log_dir(),
]
argument_sets.append(arguments)

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48 changes: 31 additions & 17 deletions pvactools/lib/prediction_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,11 @@ def check_iedb_api_response_matches(self, input_file, response_text, epitope_len
return (input_peptides == output_peptides, input_peptides, output_peptides)


def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None):
def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None, log_dir=None):
if log_dir is not None:
log_file = os.path.join(log_dir, "iedb.log")
else:
log_file = None
if iedb_executable_path is not None:
arguments = [sys.executable]
arguments.extend(self.iedb_executable_params(iedb_executable_path, self.iedb_prediction_method, allele, input_file, epitope_length))
Expand All @@ -93,12 +97,17 @@ def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb
retries = 0
while (response.status_code == 500 or response.status_code == 403 or not peptides_match) and retries < iedb_retries:
if response.status_code == 200 and not peptides_match:
print("IEDB API Output doesn't match input. Retrying.")
print(datetime.now())
print("Inputs:")
print(data)
print("Output:")
print(response.text)
log_text = "IEDB API Output doesn't match input. Retrying.\n"
log_text += "{}\n".format(datetime.now())
log_text += "Inputs:\n"
log_text += "{}\n".format(data)
log_text += "Output:\n"
log_text += "{}\n".format(response.text)
if log_file:
with open(log_file, "a") as log_fh:
log_fh.write(log_text)
else:
print(log_text)

random.seed(uuid.uuid4().int)
time.sleep(random.randint(30,90) * retries)
Expand All @@ -110,12 +119,17 @@ def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb
if response.status_code != 200:
sys.exit("Error posting request to IEDB.\n%s" % response.text)
if not peptides_match:
print("Error. IEDB API Output doesn't match input and number of retries exceeded.")
print(datetime.now())
print("Inputs:")
print(data)
print("Output:")
print(response.text)
log_text = "Error. IEDB API Output doesn't match input and number of retries exceeded."
log_text += "{}\n".format(datetime.now())
log_text += "Inputs:\n"
log_text += "{}\n".format(data)
log_text += "Output:\n"
log_text += "{}\n".format(response.text)
if log_file:
with open(log_file, "a") as log_fh:
log_fh.write(log_text)
else:
print(log_text)
sys.exit("Error. IEDB API Output doesn't match input and number of retries exceeded.")

output_mode = 'w'
Expand All @@ -132,7 +146,7 @@ def valid_allele_names_for_class(self, class_type):
with open(alleles_file_name, 'r') as fh:
return list(filter(None, fh.read().split('\n')))

def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, class_type, tmp_dir=None):
def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, class_type, tmp_dir=None, log_dir=None):
tmp_output_file = tempfile.NamedTemporaryFile('r', dir=tmp_dir, delete=False)
script = os.path.join(os.path.dirname(os.path.realpath(__file__)), "call_mhcnuggets.py")
arguments = ["python", script, input_file, allele, str(epitope_length), class_type, tmp_output_file.name]
Expand Down Expand Up @@ -343,7 +357,7 @@ def determine_neoepitopes(self, sequence, length):
epitopes[i+1] = sequence[i:i+length]
return epitopes

def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None):
def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None, log_dir=None):
results = pd.DataFrame()
all_epitopes = []
for record in SeqIO.parse(input_file, "fasta"):
Expand Down Expand Up @@ -401,7 +415,7 @@ def valid_lengths_for_allele(self, allele):
def mhcnuggets_allele(self, allele):
return allele.replace('*', '')

def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None):
def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None, log_dir=None):
return MHCnuggets.predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, 'I', tmp_dir=tmp_dir)

class IEDBMHCI(MHCI, IEDB, metaclass=ABCMeta):
Expand Down Expand Up @@ -495,7 +509,7 @@ def valid_lengths_for_allele(self, allele):
def mhcnuggets_allele(self,allele):
return "HLA-{}".format(allele).replace('*', '')

def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None):
def predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, tmp_dir=None, log_dir=None):
return MHCnuggets.predict(self, input_file, allele, epitope_length, iedb_executable_path, iedb_retries, 'II', tmp_dir=tmp_dir)

class IEDBMHCII(MHCII, IEDB, metaclass=ABCMeta):
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