From 672afedfe18bf9f1644366e55e2c2623f6d89fe8 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 27 Jan 2018 22:22:50 -0500
Subject: [PATCH] update
---
downloads-generation/models_class1/GENERATE.sh | 3 ++-
mhcflurry/class1_affinity_predictor.py | 14 +++++---------
mhcflurry/train_allele_specific_models_command.py | 10 +++++++++-
3 files changed, 16 insertions(+), 11 deletions(-)
diff --git a/downloads-generation/models_class1/GENERATE.sh b/downloads-generation/models_class1/GENERATE.sh
index 8e4905fa..a63b17de 100755
--- a/downloads-generation/models_class1/GENERATE.sh
+++ b/downloads-generation/models_class1/GENERATE.sh
@@ -37,7 +37,8 @@ time mhcflurry-class1-train-allele-specific-models \
--out-models-dir models \
--percent-rank-calibration-num-peptides-per-length 1000000 \
--min-measurements-per-allele 75 \
- --parallelization-num-jobs 0
+ --train-num-jobs 0 \
+ --calibration-num-jobs 4
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index aee7d2e5..88c807af 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -933,11 +933,6 @@ class Class1AffinityPredictor(object):
if worker_pool and len(alleles) > 1:
# Run in parallel
-
- # Performance hack.
- for network in self.neural_networks:
- network.peptides_to_network_input(encoded_peptides)
-
do_work = partial(
_calibrate_percentile_ranks,
predictor=self,
@@ -969,13 +964,14 @@ def _calibrate_percentile_ranks(alleles, predictor, peptides, bins):
Parameters
----------
- alleles
- predictor
- peptides
- bins
+ alleles : list of string
+ predictor : Class1AffinityPredictor
+ peptides : list of string or EncodableSequences
+ bins : object
Returns
-------
+ dict : allele -> percentile rank transform
"""
result = {}
diff --git a/mhcflurry/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
index dfd77d4c..406da3e0 100644
--- a/mhcflurry/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -85,7 +85,15 @@ parser.add_argument(
help="Keras verbosity. Default: %(default)s",
default=0)
parser.add_argument(
- "--parallelization-num-jobs",
+ "--train-num-jobs",
+ default=1,
+ type=int,
+ metavar="N",
+ help="Parallelization jobs. Experimental. "
+ "Set to 1 for serial run. Set to 0 to use number of cores. "
+ "Default: %(default)s.")
+parser.add_argument(
+ "--calibration-num-jobs",
default=1,
type=int,
metavar="N",
--
GitLab