From bbba5e7d1814c2c537b091077dfd814750465e2c Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 9 Feb 2018 20:15:36 -0500
Subject: [PATCH] fix
---
mhcflurry/train_allele_specific_models_command.py | 15 +++------------
1 file changed, 3 insertions(+), 12 deletions(-)
diff --git a/mhcflurry/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
index 40717a7d..dd180995 100644
--- a/mhcflurry/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -67,11 +67,6 @@ parser.add_argument(
metavar="N",
default=50,
help="Train models for alleles with >=N measurements.")
-parser.add_argument(
- "--only-quantitative",
- action="store_true",
- default=False,
- help="Use only quantitative training data")
parser.add_argument(
"--ignore-inequalities",
action="store_true",
@@ -155,17 +150,13 @@ def run(argv=sys.argv[1:]):
]
print("Subselected to 8-15mers: %s" % (str(df.shape)))
- if args.only_quantitative:
- df = df.loc[
- df.measurement_type == "quantitative"
- ]
- 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()
+ # Allele counts are in terms of quantitative data only.
+ allele_counts = (
+ df.loc[df.measurement_type == "quantitative"].allele.value_counts())
if args.allele:
alleles = [normalize_allele_name(a) for a in args.allele]
--
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