From 5737ed7a1bbdbbd662aa085951255bc9dae8868e Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 21 May 2017 21:33:39 -0400
Subject: [PATCH] fixes
---
.../class1_affinity_predictor.py | 20 +++++++++++--------
test/test_class1_binding_predictor_A0205.py | 12 ++++++++++-
2 files changed, 23 insertions(+), 9 deletions(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
index 42305241..82ea3f70 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
@@ -256,7 +256,7 @@ class Class1AffinityPredictor(object):
'peptide': peptides,
'allele': alleles,
})
- df["normalized_allele"] = input_df.allele.map(
+ df["normalized_allele"] = df.allele.map(
mhcnames.normalize_allele_name)
if self.class1_pan_allele_models:
@@ -283,13 +283,17 @@ class Class1AffinityPredictor(object):
df_predictions = df[
[c for c in df.columns if c.startswith("model_")]
]
- log_means = numpy.log(df_predictions).mean(1)
+ logs = numpy.log(df_predictions)
+ log_means = logs.mean(1)
df["prediction"] = numpy.exp(log_means)
- df["prediction_low"] = numpy.exp(log_means.quantile(q=.05, axis=1))
- df["prediction_high"] = numpy.exp(log_means.quantile(q=.05, axis=1))
+ df["prediction_low"] = numpy.exp(logs.quantile(0.05, axis=1))
+ df["prediction_high"] = numpy.exp(logs.quantile(0.95, axis=1))
+ del df["normalized_allele"]
if include_individual_model_predictions:
- return df
- return df[
- [c for c in df.columns if c not in df_predictions.columns]
- ]
\ No newline at end of file
+ columns = sorted(df.columns, key=lambda c: c.startswith('model_'))
+ else:
+ columns = [
+ c for c in df.columns if c not in df_predictions.columns
+ ]
+ return df[columns]
\ No newline at end of file
diff --git a/test/test_class1_binding_predictor_A0205.py b/test/test_class1_binding_predictor_A0205.py
index fc486469..fcdcd274 100644
--- a/test/test_class1_binding_predictor_A0205.py
+++ b/test/test_class1_binding_predictor_A0205.py
@@ -49,7 +49,7 @@ def test_class1_neural_network_A0205_training_accuracy():
def test_class1_neural_network_A0205_training_accuracy():
predictor = Class1AffinityPredictor()
predictor.fit_allele_specific_predictors(
- n_models=1,
+ n_models=2,
architecture_hyperparameters=hyperparameters,
allele=allele,
peptides=df.peptide.values,
@@ -64,3 +64,13 @@ def test_class1_neural_network_A0205_training_accuracy():
rtol=0.2,
atol=0.2)
+ ic50_pred_df = predictor.predict_to_dataframe(
+ df.peptide.values, allele=allele)
+ print(ic50_pred_df)
+
+ ic50_pred_df2 = predictor.predict_to_dataframe(
+ df.peptide.values,
+ allele=allele,
+ include_individual_model_predictions=True)
+ print(ic50_pred_df2)
+
--
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