From a59fe5054461f739fd778a486fa46b1a94066c86 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Tue, 19 Apr 2016 13:35:04 -0400
Subject: [PATCH] added known epitope tests
---
mhcflurry/predictor_base.py | 5 +++++
test/test_known_class1_epitopes.py | 30 ++++++++++++++++++++++++++++--
2 files changed, 33 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/predictor_base.py b/mhcflurry/predictor_base.py
index 4b104049..1c6ed73a 100644
--- a/mhcflurry/predictor_base.py
+++ b/mhcflurry/predictor_base.py
@@ -15,6 +15,7 @@
from collections import defaultdict
import numpy as np
+from six import string_types
from .peptide_encoding import fixed_length_index_encoding
from .amino_acid import (
@@ -114,6 +115,10 @@ class PredictorBase(object):
amino acid characters. The prediction for a single peptide will be
the average of expanded 9mers.
"""
+ if isinstance(peptides, string_types):
+ raise TypeError("Input must be a list of peptides, not %s : %s" % (
+ peptides, type(peptides)))
+
input_matrix, original_peptide_indices = self.encode_peptides(peptides)
# non-9mer peptides get multiple predictions, which are then combined
# with the combine_fn argument
diff --git a/test/test_known_class1_epitopes.py b/test/test_known_class1_epitopes.py
index 8b7ac11e..face8d3a 100644
--- a/test/test_known_class1_epitopes.py
+++ b/test/test_known_class1_epitopes.py
@@ -1,3 +1,29 @@
-def test_known_class1_epitopes():
- pass
+from mhcflurry import Class1BindingPredictor
+
+def test_MAGE_epitope():
+ # Test the A1 MAGE epitope ESDPIVAQY from
+ # Identification of a Titin-Derived HLA-A1-Presented Peptide
+ # as a Cross-Reactive Target for Engineered MAGE A3-Directed
+ # T Cells
+ model = Class1BindingPredictor.from_allele_name("HLA-A*01:01")
+ ic50s = model.predict_peptides_ic50(["ESDPIVAQY"])
+ print(ic50s)
+ assert len(ic50s) == 1
+ ic50 = ic50s[0]
+ assert ic50 <= 500
+
+def test_HIV_epitope():
+ # Test the A2 HIV epitope SLYNTVATL from
+ # The HIV-1 HLA-A2-SLYNTVATL Is a Help-Independent CTL Epitope
+ model = Class1BindingPredictor.from_allele_name("HLA-A*02:01")
+ ic50s = model.predict_peptides_ic50(["SLYNTVATL"])
+ print(ic50s)
+ assert len(ic50s) == 1
+ ic50 = ic50s[0]
+ assert ic50 <= 500
+
+
+if __name__ == "__main__":
+ test_MAGE_epitope()
+ test_HIV_epitope()
--
GitLab