From bbfd350d889a2cb7f2871aa5380bac7a61f7af05 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 25 Jan 2018 19:32:14 -0500
Subject: [PATCH] support for inequalities in train command
---
.../models_class1_no_mass_spec/GENERATE.sh | 4 +++-
mhcflurry/train_allele_specific_models_command.py | 12 ++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/downloads-generation/models_class1_no_mass_spec/GENERATE.sh b/downloads-generation/models_class1_no_mass_spec/GENERATE.sh
index 3b80f704..00a6233b 100755
--- a/downloads-generation/models_class1_no_mass_spec/GENERATE.sh
+++ b/downloads-generation/models_class1_no_mass_spec/GENERATE.sh
@@ -36,7 +36,9 @@ time mhcflurry-class1-train-allele-specific-models \
--hyperparameters hyperparameters.yaml \
--out-models-dir models \
--percent-rank-calibration-num-peptides-per-length 1000000 \
- --min-measurements-per-allele 75
+ --min-measurements-per-allele 75 \
+ --ignore-inequalities
+
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
diff --git a/mhcflurry/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
index b095e6a4..8d63b4f3 100644
--- a/mhcflurry/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -52,6 +52,11 @@ parser.add_argument(
action="store_true",
default=False,
help="Use only quantitative training data")
+parser.add_argument(
+ "--ignore-inequalities",
+ action="store_true",
+ default=False,
+ help="Do not use affinity value inequalities even when present in data")
parser.add_argument(
"--percent-rank-calibration-num-peptides-per-length",
type=int,
@@ -115,6 +120,10 @@ def run(argv=sys.argv[1:]):
]
print("Subselected to quantitative: %s" % (str(df.shape)))
+ if args.ignore_inequalities and "measurement_inequality" in df.columns:
+ print("Dropping measurement_inequality column")
+ del df["measurement_inequality"]
+
allele_counts = df.allele.value_counts()
if args.allele:
@@ -263,6 +272,9 @@ def process_work(
allele=allele,
peptides=train_data.peptide.values,
affinities=train_data.measurement_value.values,
+ inequalities=(
+ train_data.measurement_inequality.values
+ if "measurement_inequality" in train_data.columns else None),
models_dir_for_save=save_to,
progress_preamble=progress_preamble,
verbose=verbose)
--
GitLab