From 1cae85f6d29595ca2d34660b126247219587b989 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 28 Jan 2018 15:17:51 -0500
Subject: [PATCH] cache peptide encoding in percentile rank calibration
---
mhcflurry/class1_affinity_predictor.py | 2 +-
mhcflurry/train_allele_specific_models_command.py | 3 ++-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 1bbefd41..fa2023eb 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -933,7 +933,7 @@ class Class1AffinityPredictor(object):
encoded_peptides = EncodableSequences.create(peptides)
for (i, allele) in enumerate(alleles):
- predictions = self.predict(peptides, allele=allele)
+ predictions = self.predict(encoded_peptides, allele=allele)
transform = PercentRankTransform()
transform.fit(predictions, bins=bins)
self.allele_to_percent_rank_transform[allele] = transform
diff --git a/mhcflurry/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
index 87fe6b01..3d72b32a 100644
--- a/mhcflurry/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -9,6 +9,7 @@ import time
import traceback
from multiprocessing import Pool
from functools import partial
+from pprint import pprint
import pandas
import yaml
@@ -363,7 +364,7 @@ def train_model(
# For the first model for the first allele, print the architecture.
print("*** HYPERPARAMETER SET %d***" %
(hyperparameter_set_num + 1))
- print(hyperparameters)
+ pprint(hyperparameters)
print("*** ARCHITECTURE FOR HYPERPARAMETER SET %d***" %
(hyperparameter_set_num + 1))
model.network(borrow=True).summary()
--
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