From d28248d897dffb80e9dd8a403faca8415044ae58 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 6 Sep 2019 09:39:57 -0400
Subject: [PATCH] theano on python 2.7 fixes; pylint fixes
---
downloads-generation/allele_sequences/filter_sequences.py | 2 +-
.../allele_sequences/make_allele_sequences.py | 2 +-
mhcflurry/class1_neural_network.py | 7 ++++---
mhcflurry/train_pan_allele_models_command.py | 2 +-
4 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/allele_sequences/filter_sequences.py b/downloads-generation/allele_sequences/filter_sequences.py
index 282fdd53..2d92a0b9 100644
--- a/downloads-generation/allele_sequences/filter_sequences.py
+++ b/downloads-generation/allele_sequences/filter_sequences.py
@@ -8,7 +8,7 @@ import argparse
import mhcnames
-import Bio.SeqIO
+import Bio.SeqIO # pylint: disable=import-error
def normalize(s, disallowed=["MIC", "HFE"]):
diff --git a/downloads-generation/allele_sequences/make_allele_sequences.py b/downloads-generation/allele_sequences/make_allele_sequences.py
index 899eb42d..d984dd34 100644
--- a/downloads-generation/allele_sequences/make_allele_sequences.py
+++ b/downloads-generation/allele_sequences/make_allele_sequences.py
@@ -13,7 +13,7 @@ import pandas
import mhcnames
-import Bio.SeqIO
+import Bio.SeqIO # pylint: disable=import-error
def normalize_simple(s):
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index f23ca977..31a433b2 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -1126,6 +1126,7 @@ class Class1NeuralNetwork(object):
"""
import keras
+ import keras.backend as K
from keras.layers import Input
from keras.models import Model
@@ -1162,7 +1163,7 @@ class Class1NeuralNetwork(object):
# Merging an ensemble of pan-allele architectures
network = networks[0]
peptide_input = Input(
- shape=tuple(int(x) for x in network.inputs[0].shape[1:]),
+ shape=tuple(int(x) for x in K.int_shape(network.inputs[0])[1:]),
dtype='float32',
name='peptide')
allele_input = Input(
@@ -1366,7 +1367,7 @@ class Class1NeuralNetwork(object):
l is the allele sequence length,
m is the length of the vectors used to represent amino acids
"""
- from keras.models import model_from_json
+ from keras.models import clone_model
reshaped = allele_representations.reshape(
(allele_representations.shape[0], -1))
original_model = self.network()
@@ -1392,7 +1393,7 @@ class Class1NeuralNetwork(object):
# Network surgery required. Make a new network with this layer's
# dimensions changed. Kind of a hack.
layer.input_dim = reshaped.shape[0]
- new_model = model_from_json(original_model.to_json())
+ new_model = clone_model(original_model)
# copy weights for other layers over
for layer in new_model.layers:
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index a985539d..c1b015e4 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -270,7 +270,7 @@ def run(argv=sys.argv[1:]):
return main(args)
except Exception as e:
print(e)
- import ipdb
+ import ipdb # pylint: disable=import-error
ipdb.set_trace()
raise
else:
--
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