From 79e76cf9c9d34506cf25cc6d51edcb43765a3ae2 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Wed, 1 Jul 2015 16:51:25 -0400
Subject: [PATCH] added web API and python3 compat
---
mhcflurry/common.py | 6 +++
mhcflurry/data_helpers.py | 6 +++
mhcflurry/feedforward.py | 6 +++
mhcflurry/mhc1_binding_predictor.py | 10 ++--
scripts/create-combined-class1-dataset.py | 6 +++
scripts/mhcflurry-class1-web-server.py | 51 +++++++++++++++++++
scripts/mhcflurry-class1.py | 21 ++++----
.../train-class1-allele-specific-models.py | 6 +++
8 files changed, 98 insertions(+), 14 deletions(-)
create mode 100755 scripts/mhcflurry-class1-web-server.py
diff --git a/mhcflurry/common.py b/mhcflurry/common.py
index 65cbb9e8..7ff1bdcc 100644
--- a/mhcflurry/common.py
+++ b/mhcflurry/common.py
@@ -12,6 +12,12 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+)
+
def parse_int_list(s):
return [int(part.strip() for part in s.split(","))]
diff --git a/mhcflurry/data_helpers.py b/mhcflurry/data_helpers.py
index b9b36248..7d7d5e1f 100644
--- a/mhcflurry/data_helpers.py
+++ b/mhcflurry/data_helpers.py
@@ -12,7 +12,13 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+)
from collections import namedtuple
+
import pandas as pd
import numpy as np
diff --git a/mhcflurry/feedforward.py b/mhcflurry/feedforward.py
index 7e3b850d..f9072d8c 100644
--- a/mhcflurry/feedforward.py
+++ b/mhcflurry/feedforward.py
@@ -12,6 +12,12 @@
# See the License for the specific language governing permissions and
# limitations under the License.
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+)
+
import keras
from keras.models import Sequential
from keras.layers.core import Dense, Activation, Flatten, Dropout
diff --git a/mhcflurry/mhc1_binding_predictor.py b/mhcflurry/mhc1_binding_predictor.py
index d3e437e5..3a2061a8 100644
--- a/mhcflurry/mhc1_binding_predictor.py
+++ b/mhcflurry/mhc1_binding_predictor.py
@@ -15,7 +15,11 @@
"""
Allele specific MHC Class I binding affinity predictor
"""
-
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+)
from os import listdir
from os.path import exists, join
from itertools import groupby
@@ -110,7 +114,7 @@ class Mhc1BindingPredictor(object):
return [
peptide[:i] + extra_amino_acid + peptide[i:]
for peptide in peptides
- for i in xrange(3, 8)
+ for i in range(3, 8)
for extra_amino_acid in amino_acid_letters
]
else:
@@ -141,7 +145,7 @@ class Mhc1BindingPredictor(object):
raw_y = self._predict_9mer_peptides(expanded_peptides)
median_y = np.zeros(n_group)
# take the median of each group of log(IC50) values
- for i in xrange(n_group):
+ for i in range(n_group):
start = i * expansion_factor
end = (i + 1) * expansion_factor
median_y[i] = np.median(raw_y[start:end])
diff --git a/scripts/create-combined-class1-dataset.py b/scripts/create-combined-class1-dataset.py
index 4544b819..cf8bbb62 100755
--- a/scripts/create-combined-class1-dataset.py
+++ b/scripts/create-combined-class1-dataset.py
@@ -6,6 +6,12 @@ Combine 2013 Kim/Peters NetMHCpan dataset[*] with more recent IEDB entries
* = "Dataset size and composition impact the reliability..."
"""
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+ unicode_literals
+)
from os.path import join
import pickle
from collections import Counter
diff --git a/scripts/mhcflurry-class1-web-server.py b/scripts/mhcflurry-class1-web-server.py
new file mode 100755
index 00000000..ef2067b8
--- /dev/null
+++ b/scripts/mhcflurry-class1-web-server.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+# Copyright (c) 2015. 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.
+
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+ unicode_literals
+)
+import argparse
+
+from bottle import post, request, run
+
+from mhcflurry.common import (
+ split_uppercase_sequences,
+ split_allele_names,
+)
+from mhcflurry.class1 import predict
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument("--host", default="0.0.0.0")
+parser.add_argument("--port", default=80, type=int)
+parser.add_argument("--debug", default=False, action="store_true")
+
+
+@post('/')
+def get_binding_value():
+ peptides_string = request.forms.get('peptide')
+ peptides_list = split_uppercase_sequences(peptides_string)
+ alleles_string = request.forms.get('allele')
+ alleles_list = split_allele_names(alleles_string)
+ result_df = predict(alleles=alleles_list, peptides=peptides_list)
+ return result_df.to_csv(sep="\t", index=False)
+
+if __name__ == "__main__":
+ args = parser.parse_args()
+ run(host=args.host, port=args.port, debug=args.debug)
\ No newline at end of file
diff --git a/scripts/mhcflurry-class1.py b/scripts/mhcflurry-class1.py
index a4f480d9..d1a92458 100755
--- a/scripts/mhcflurry-class1.py
+++ b/scripts/mhcflurry-class1.py
@@ -15,16 +15,20 @@
# limitations under the License.
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+ # unicode_literals
+)
import argparse
-import pandas as pd
-
from mhcflurry.common import (
parse_int_list,
split_uppercase_sequences,
- split_allele_names
+ split_allele_names,
)
-from mhcflurry import Mhc1BindingPredictor
+from mhcflurry.class1 import predict
parser = argparse.ArgumentParser()
@@ -48,10 +52,5 @@ parser.add_argument("--peptide-lengths",
if __name__ == "__main__":
args = parser.parse_args()
- allele_dataframes = []
- for allele in args.mhc:
- model = Mhc1BindingPredictor(allele=allele)
- df = model.predict_peptides(args.sequence)
- allele_dataframes.append(df)
- combined = pd.concat(allele_dataframes)
- print combined
+ df = predict(alleles=args.mhc, peptides=args.sequence)
+ print(df.to_csv(sep="\t", index=False), end="")
diff --git a/scripts/train-class1-allele-specific-models.py b/scripts/train-class1-allele-specific-models.py
index e422588c..784e8ca2 100755
--- a/scripts/train-class1-allele-specific-models.py
+++ b/scripts/train-class1-allele-specific-models.py
@@ -17,6 +17,12 @@ Using the following hyperparameters:
Nielsen 2009 dataset.
"""
+from __future__ import (
+ print_function,
+ division,
+ absolute_import,
+ unicode_literals
+)
from shutil import rmtree
from os import makedirs
from os.path import exists, join
--
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