From 72682443982480afcf29b3e823490930e66620cc Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Tue, 1 Oct 2019 08:11:31 -0400
Subject: [PATCH] fix
---
.../data_mass_spec_benchmark/run_mhcflurry.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
index 84fb4fe5..e2421d82 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
@@ -7,6 +7,7 @@ import sys
import time
import traceback
import collections
+import math
from functools import partial
import numpy
@@ -100,7 +101,8 @@ def run(argv=sys.argv[1:]):
# using local parallelism.
predictor = Class1AffinityPredictor.load(
args.models_dir,
- optimization_level=None if serial_run or args.cluster_parallelism else 0,
+ #optimization_level=None if serial_run or args.cluster_parallelism else 0,
+ optimization_level=0,
)
alleles = [normalize_allele_name(a) for a in args.allele]
@@ -133,7 +135,7 @@ def run(argv=sys.argv[1:]):
}).to_csv(out_alleles, index=False)
print("Wrote: ", out_alleles)
- num_chunks = int(len(peptides) / args.chunk_size)
+ num_chunks = int(math.ceil(len(peptides) / args.chunk_size))
print("Split peptides into %d chunks" % num_chunks)
peptide_chunks = numpy.array_split(peptides, num_chunks)
--
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