From 09dd0cd902b59c38221696a6e1c6f35cc095a582 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 3 Dec 2019 17:56:33 -0500
Subject: [PATCH] renames
---
mhcflurry/batch_generator.py | 2 +-
mhcflurry/class1_presentation_neural_network.py | 17 +++++++++--------
mhcflurry/class1_presentation_predictor.py | 4 ++--
mhcflurry/multiallelic_refinement_command.py | 10 +++++-----
test/test_class1_presentation_predictor.py | 1 -
5 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/mhcflurry/batch_generator.py b/mhcflurry/batch_generator.py
index 570cc8ad..ca512072 100644
--- a/mhcflurry/batch_generator.py
+++ b/mhcflurry/batch_generator.py
@@ -103,7 +103,7 @@ class MultiallelicMassSpecBatchGenerator(object):
batch_generator_batch_size=128,
batch_generator_affinity_fraction=0.5)
"""
- Hyperperameters for batch generation for the ligandome predictor.
+ Hyperperameters for batch generation for the presentation predictor.
"""
def __init__(self, hyperparameters):
diff --git a/mhcflurry/class1_presentation_neural_network.py b/mhcflurry/class1_presentation_neural_network.py
index db3a2535..897fafd8 100644
--- a/mhcflurry/class1_presentation_neural_network.py
+++ b/mhcflurry/class1_presentation_neural_network.py
@@ -195,22 +195,23 @@ class Class1PresentationNeuralNetwork(object):
[node, auxiliary_input], name="affinities_with_auxiliary")
layer = Dense(8, activation="tanh")
- lifted = TimeDistributed(layer, name="ligandome_hidden1")
+ lifted = TimeDistributed(layer, name="presentation_hidden1")
node = lifted(node)
layer = Dense(1, activation="tanh")
- lifted = TimeDistributed(layer, name="ligandome_output")
- ligandome_adjustment = lifted(node)
+ lifted = TimeDistributed(layer, name="presentation_hidden2")
+ presentation_adjustment = lifted(node)
def logit(x):
import tensorflow as tf
return - tf.log(1. / x - 1.)
- ligandome_output_pre_sigmoid = Add()([
+ presentation_output_pre_sigmoid = Add()([
Lambda(logit)(affinity_predictor_matrix_output),
- ligandome_adjustment,
+ presentation_adjustment,
])
- ligandome_output = Activation("sigmoid")(ligandome_output_pre_sigmoid)
+ presentation_output = Activation("sigmoid", name="presentation_output")(
+ presentation_output_pre_sigmoid)
self.network = Model(
inputs=[
@@ -219,10 +220,10 @@ class Class1PresentationNeuralNetwork(object):
] + ([] if auxiliary_input is None else [auxiliary_input]),
outputs=[
affinity_predictor_output,
- ligandome_output,
+ presentation_output,
affinity_predictor_matrix_output
],
- name="ligandome",
+ name="presentation",
)
self.network.summary()
diff --git a/mhcflurry/class1_presentation_predictor.py b/mhcflurry/class1_presentation_predictor.py
index 1471ad97..625b32f4 100644
--- a/mhcflurry/class1_presentation_predictor.py
+++ b/mhcflurry/class1_presentation_predictor.py
@@ -36,11 +36,11 @@ from .custom_loss import (
class Class1PresentationPredictor(object):
def __init__(
self,
- class1_ligandome_neural_networks,
+ class1_presentation_neural_networks,
allele_to_sequence,
manifest_df=None,
metadata_dataframes=None):
- self.networks = class1_ligandome_neural_networks
+ self.networks = class1_presentation_neural_networks
self.allele_to_sequence = allele_to_sequence
self._manifest_df = manifest_df
self.metadata_dataframes = (
diff --git a/mhcflurry/multiallelic_refinement_command.py b/mhcflurry/multiallelic_refinement_command.py
index 1e47e77f..324efff0 100644
--- a/mhcflurry/multiallelic_refinement_command.py
+++ b/mhcflurry/multiallelic_refinement_command.py
@@ -57,17 +57,17 @@ parser.add_argument(
parser.add_argument(
"--hyperparameters",
metavar="FILE.json",
- help="Ligandome predictor hyperparameters")
+ help="presentation predictor hyperparameters")
parser.add_argument(
"--out-affinity-predictor-dir",
metavar="DIR",
required=True,
help="Directory to write refined models")
parser.add_argument(
- "--out-ligandome-predictor-dir",
+ "--out-presentation-predictor-dir",
metavar="DIR",
required=True,
- help="Directory to write ligandome predictors")
+ help="Directory to write preentation predictor")
parser.add_argument(
"--verbosity",
type=int,
@@ -89,8 +89,8 @@ def run(argv=sys.argv[1:]):
args.out_affinity_predictor_dir = os.path.abspath(
args.out_affinity_predictor_dir)
- args.out_ligandome_predictor_dir = os.path.abspath(
- args.out_ligandome_predictor_dir)
+ args.out_presentation_predictor_dir = os.path.abspath(
+ args.out_presentation_predictor_dir)
configure_logging(verbose=args.verbosity > 1)
diff --git a/test/test_class1_presentation_predictor.py b/test/test_class1_presentation_predictor.py
index 768d270a..bbd0bf1e 100644
--- a/test/test_class1_presentation_predictor.py
+++ b/test/test_class1_presentation_predictor.py
@@ -56,7 +56,6 @@ def data_path(name):
return os.path.join(os.path.dirname(__file__), "data", name)
-
def setup():
global PAN_ALLELE_PREDICTOR_NO_MASS_SPEC
global PAN_ALLELE_MOTIFS_WITH_MASS_SPEC_DF
--
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