From 5a66b6fa285f3ea459423e1a7b473f8fcfdc2a8b Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Fri, 6 May 2016 16:06:24 -0400
Subject: [PATCH] fixed class1_binding_predictor tests
---
...llele_specific_kmer_ic50_predictor_base.py | 5 +-
mhcflurry/class1_binding_predictor.py | 2 +-
mhcflurry/dataset.py | 3 +-
test/dummy_predictors.py | 48 -------------------
...s1_binding_predictor_with_dummy_models.py} | 2 +-
5 files changed, 7 insertions(+), 53 deletions(-)
delete mode 100644 test/dummy_predictors.py
rename test/{test_class1_binding_predictor.py => test_class1_binding_predictor_with_dummy_models.py} (97%)
diff --git a/mhcflurry/class1_allele_specific_kmer_ic50_predictor_base.py b/mhcflurry/class1_allele_specific_kmer_ic50_predictor_base.py
index d2dea373..ee244da1 100644
--- a/mhcflurry/class1_allele_specific_kmer_ic50_predictor_base.py
+++ b/mhcflurry/class1_allele_specific_kmer_ic50_predictor_base.py
@@ -109,7 +109,7 @@ class Class1AlleleSpecificKmerIC50PredictorBase(IC50PredictorBase):
if any(len(peptide) != self.kmer_size for peptide in peptides):
raise ValueError("Can only predict 9mer peptides")
X, _ = self.encode_peptides(peptides)
- return self.predict_scores_for_kmer_array(X)
+ return self.predict_scores_for_kmer_encoded_array(X)
def predict_kmer_peptides_ic50(self, peptides):
scores = self.predict_scores_for_kmer_peptides(peptides)
@@ -132,7 +132,8 @@ class Class1AlleleSpecificKmerIC50PredictorBase(IC50PredictorBase):
# peptides of lengths other than self.kmer_size get multiple predictions,
# which are then combined with the combine_fn argument
multiple_predictions_dict = defaultdict(list)
- fixed_length_predictions = self.predict(input_matrix)
+ fixed_length_predictions = \
+ self.predict_scores_for_kmer_encoded_array(input_matrix)
for i, yi in enumerate(fixed_length_predictions):
original_peptide_index = original_peptide_indices[i]
original_peptide = peptides[original_peptide_index]
diff --git a/mhcflurry/class1_binding_predictor.py b/mhcflurry/class1_binding_predictor.py
index 1f1f9f97..027b5772 100644
--- a/mhcflurry/class1_binding_predictor.py
+++ b/mhcflurry/class1_binding_predictor.py
@@ -314,7 +314,7 @@ class Class1BindingPredictor(Class1AlleleSpecificKmerIC50PredictorBase):
alleles = alleles_with_models.intersection(alleles_with_weights)
return list(sorted(alleles))
- def predict_scores_for_kmer_array(self, X):
+ def predict_scores_for_kmer_encoded_array(self, X):
"""
Given an encoded array of amino acid indices, returns a vector
of predicted log IC50 values.
diff --git a/mhcflurry/dataset.py b/mhcflurry/dataset.py
index afb801de..b8f08bfb 100644
--- a/mhcflurry/dataset.py
+++ b/mhcflurry/dataset.py
@@ -62,7 +62,7 @@ class Dataset(object):
# make allele and peptide columns the index, and copy it
# so we can add a column without any observable side-effect in
# the calling code
- df = df.set_index(["allele", "peptide"])
+ df = df.set_index(["allele", "peptide"], drop=False)
if "sample_weight" not in columns:
df["sample_weight"] = np.ones(len(df), dtype=float)
@@ -209,6 +209,7 @@ class Dataset(object):
"Wrong length for column '%s', expected %d but got %d" % (
column_name, column))
df[column_name] = np.asarray(column)
+ print(df)
return cls(df)
@classmethod
diff --git a/test/dummy_predictors.py b/test/dummy_predictors.py
deleted file mode 100644
index 0ea99cca..00000000
--- a/test/dummy_predictors.py
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright (c) 2016. Mount Sinai School of Medicine
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import numpy as np
-from mhcflurry import Class1BindingPredictor
-
-class Dummy9merIndexEncodingModel(object):
- """
- Dummy molde used for testing the pMHC binding predictor.
- """
- def __init__(self, constant_output_value=0):
- self.constant_output_value = constant_output_value
-
- def predict(self, X, verbose=False):
- assert isinstance(X, np.ndarray)
- assert len(X.shape) == 2
- n_rows, n_cols = X.shape
- n_cols == 9, "Expected 9mer index input input, got %d columns" % (
- n_cols,)
- return np.ones(n_rows, dtype=float) * self.constant_output_value
-
-always_zero_predictor_with_unknown_AAs = Class1BindingPredictor(
- model=Dummy9merIndexEncodingModel(0),
- allow_unknown_amino_acids=True)
-
-always_zero_predictor_without_unknown_AAs = Class1BindingPredictor(
- model=Dummy9merIndexEncodingModel(0),
- allow_unknown_amino_acids=False)
-
-
-always_one_predictor_with_unknown_AAs = Class1BindingPredictor(
- model=Dummy9merIndexEncodingModel(1),
- allow_unknown_amino_acids=True)
-
-always_one_predictor_without_unknown_AAs = Class1BindingPredictor(
- model=Dummy9merIndexEncodingModel(1),
- allow_unknown_amino_acids=False)
diff --git a/test/test_class1_binding_predictor.py b/test/test_class1_binding_predictor_with_dummy_models.py
similarity index 97%
rename from test/test_class1_binding_predictor.py
rename to test/test_class1_binding_predictor_with_dummy_models.py
index 8a4b7c60..028926fd 100644
--- a/test/test_class1_binding_predictor.py
+++ b/test/test_class1_binding_predictor_with_dummy_models.py
@@ -15,7 +15,7 @@
import numpy as np
-from dummy_predictors import always_zero_predictor_with_unknown_AAs
+from dummy_models import always_zero_predictor_with_unknown_AAs
def test_always_zero_9mer_inputs():
--
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