"""
"""
import argparse
import os
import signal
import sys
import time
import traceback
import math
from functools import partial
import numpy
import pandas
from mhcnames import normalize_allele_name
import tqdm # progress bar
tqdm.monitor_interval = 0 # see https://github.com/tqdm/tqdm/issues/481
from mhcflurry.class1_affinity_predictor import Class1AffinityPredictor
from mhcflurry.common import configure_logging
from mhcflurry.local_parallelism import (
add_local_parallelism_args,
worker_pool_with_gpu_assignments_from_args,
call_wrapped_kwargs)
from mhcflurry.cluster_parallelism import (
add_cluster_parallelism_args,
cluster_results_from_args)
# To avoid pickling large matrices to send to child processes when running in
# parallel, we use this global variable as a place to store data. Data that is
# stored here before creating the thread pool will be inherited to the child
# processes upon fork() call, allowing us to share large data with the workers
# via shared memory.
GLOBAL_DATA = {}
parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument(
"input_peptides",
metavar="CSV",
help="CSV file with 'peptide' column")
parser.add_argument(
"--models-dir",
metavar="DIR",
required=True,
help="Directory to read MHCflurry models")
parser.add_argument(
"--allele",
default=None,
required=True,
nargs="+",
help="Alleles to predict")
parser.add_argument(
"--chunk-size",
type=int,
default=100000,
help="Num peptides per job. Default: %(default)s")
parser.add_argument(
"--batch-size",
type=int,
default=4096,
help="Keras batch size for predictions. Default: %(default)s")
parser.add_argument(
"--out",
metavar="DIR",
help="Write results to DIR")
parser.add_argument(
"--verbosity",
type=int,
help="Keras verbosity. Default: %(default)s",
default=0)
parser.add_argument(
"--max-peptides",
type=int,
help="Max peptides to process. For debugging.",
default=None)
add_local_parallelism_args(parser)
add_cluster_parallelism_args(parser)
def run(argv=sys.argv[1:]):
global GLOBAL_DATA
# On sigusr1 print stack trace
print("To show stack trace, run:\nkill -s USR1 %d" % os.getpid())
signal.signal(signal.SIGUSR1, lambda sig, frame: traceback.print_stack())
args = parser.parse_args(argv)
args.models_dir = os.path.abspath(args.models_dir)
configure_logging(verbose=args.verbosity > 1)
serial_run = not args.cluster_parallelism and args.num_jobs == 0
# It's important that we don't trigger a Keras import here since that breaks
# local parallelism (tensorflow backend). So we set optimization_level=0.
predictor = Class1AffinityPredictor.load(
args.models_dir,
optimization_level=0,
)
alleles = [normalize_allele_name(a) for a in args.allele]
alleles = sorted(set(alleles))
peptides = pandas.read_csv(
args.input_peptides, nrows=args.max_peptides).peptide.drop_duplicates()
print("Filtering to valid peptides. Starting at: ", len(peptides))
peptides = peptides[peptides.str.match("^[ACDEFGHIKLMNPQRSTVWY]+$")]
print("Filtered to: ", len(peptides))
peptides = peptides.unique()
num_peptides = len(peptides)
print("Predictions for %d alleles x %d peptides." % (
len(alleles), num_peptides))
if not os.path.exists(args.out):
print("Creating", args.out)
os.mkdir(args.out)
# Write peptide and allele lists to out dir.
out_peptides = os.path.abspath(os.path.join(args.out, "peptides.csv"))
pandas.DataFrame({"peptide": peptides}).to_csv(out_peptides, index=False)
print("Wrote: ", out_peptides)
allele_to_file_path = dict(
(allele, "%s.npz" % (allele.replace("*", ""))) for allele in alleles)
out_alleles = os.path.abspath(os.path.join(args.out, "alleles.csv"))
pandas.DataFrame({
'allele': alleles,
'path': [allele_to_file_path[allele] for allele in alleles],
}).to_csv(out_alleles, index=False)
print("Wrote: ", out_alleles)
num_chunks = int(math.ceil(len(peptides) / args.chunk_size))
print("Splitting peptides into %d chunks" % num_chunks)
peptide_chunks = numpy.array_split(peptides, num_chunks)
GLOBAL_DATA["predictor"] = predictor
GLOBAL_DATA["args"] = {
'verbose': args.verbosity > 0,
'model_kwargs': {
'batch_size': args.batch_size,
}
}
work_items = []
for (chunk_index, chunk_peptides) in enumerate(peptide_chunks):
work_item = {
'alleles': alleles,
'chunk_index': chunk_index,
'peptides': chunk_peptides,
}
work_items.append(work_item)
print("Work items: ", len(work_items))
worker_pool = None
start = time.time()
if serial_run:
# Serial run
print("Running in serial.")
results = (
do_predictions(**item) for item in work_items)
elif args.cluster_parallelism:
# Run using separate processes HPC cluster.
print("Running on cluster.")
results = cluster_results_from_args(
args,
work_function=do_predictions,
work_items=work_items,
constant_data=GLOBAL_DATA,
input_serialization_method="dill",
result_serialization_method="pickle",
clear_constant_data=True)
else:
worker_pool = worker_pool_with_gpu_assignments_from_args(args)
print("Worker pool", worker_pool)
assert worker_pool is not None
results = worker_pool.imap_unordered(
partial(call_wrapped_kwargs, do_predictions),
work_items,
chunksize=1)
allele_to_chunk_index_to_predictions = {}
for allele in alleles:
allele_to_chunk_index_to_predictions[allele] = {}
for (chunk_index, allele_to_predictions) in tqdm.tqdm(
results, total=len(work_items)):
for (allele, predictions) in allele_to_predictions.items():
chunk_index_to_predictions = allele_to_chunk_index_to_predictions[
allele
]
assert chunk_index not in chunk_index_to_predictions
chunk_index_to_predictions[chunk_index] = predictions
if len(allele_to_chunk_index_to_predictions[allele]) == num_chunks:
chunk_predictions = sorted(chunk_index_to_predictions.items())
assert [i for (i, _) in chunk_predictions] == list(
range(num_chunks))
predictions = numpy.concatenate([
predictions for (_, predictions) in chunk_predictions
])
assert len(predictions) == num_peptides
out_path = os.path.join(
args.out, allele.replace("*", "")) + ".npz"
out_path = os.path.abspath(out_path)
numpy.savez(out_path, predictions)
print("Wrote:", out_path)
del allele_to_chunk_index_to_predictions[allele]
assert not allele_to_chunk_index_to_predictions, (
"Not all results written: ", allele_to_chunk_index_to_predictions)
if worker_pool:
worker_pool.close()
worker_pool.join()
prediction_time = time.time() - start
print("Done generating predictions in %0.2f min." % (
prediction_time / 60.0))
def do_predictions(chunk_index, peptides, alleles, constant_data=None):
# This may run on the cluster in a way that misses all top level imports,
# so we have to re-import everything here.
import time
from mhcflurry.encodable_sequences import EncodableSequences
if constant_data is None:
constant_data = GLOBAL_DATA
predictor = constant_data['predictor']
verbose = constant_data['args'].get("verbose", False)
model_kwargs = constant_data['args'].get("model_kwargs", {})
predictor.optimize(warn=False) # since we loaded with optimization_level=0
start = time.time()
results = {}
peptides = EncodableSequences.create(peptides)
for (i, allele) in enumerate(alleles):
print("Processing allele %d / %d: %0.2f sec elapsed" % (
i + 1, len(alleles), time.time() - start))
results[allele] = predictor.predict(
peptides=peptides,
allele=allele,
throw=False,
model_kwargs=model_kwargs).astype('float32')
print("Done predicting in", time.time() - start, "sec")
return (chunk_index, results)
if __name__ == '__main__':
run()