From 4c44b00cfb574b37733b0aa14eaf29c68e8a9b69 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Mon, 13 Jul 2015 15:18:17 -0400
Subject: [PATCH] add get URL for alleles
---
mhcflurry/class1.py | 13 +++++++++++++
.../class1_allele_specific_hyperparameters.py | 2 +-
scripts/mhcflurry-class1-web-server.py | 17 +++++++++++++----
3 files changed, 27 insertions(+), 5 deletions(-)
diff --git a/mhcflurry/class1.py b/mhcflurry/class1.py
index f90e79ec..aa099d62 100644
--- a/mhcflurry/class1.py
+++ b/mhcflurry/class1.py
@@ -1,5 +1,7 @@
import pandas as pd
+import os
+from .paths import CLASS1_MODEL_DIRECTORY
from .mhc1_binding_predictor import Mhc1BindingPredictor
def predict(alleles, peptides):
@@ -9,3 +11,14 @@ def predict(alleles, peptides):
df = model.predict_peptides(peptides)
allele_dataframes.append(df)
return pd.concat(allele_dataframes)
+
+def supported_alleles():
+ alleles = []
+ for filename in os.listdir(CLASS1_MODEL_DIRECTORY):
+ allele = filename.replace(".hdf", "")
+ if len(allele) < 5:
+ # skipping serotype names like A2 or B7
+ continue
+ allele = "HLA-%s*%s:%s" % (allele[0], allele[1:3], allele[3:])
+ alleles.append(allele)
+ return alleles
diff --git a/mhcflurry/class1_allele_specific_hyperparameters.py b/mhcflurry/class1_allele_specific_hyperparameters.py
index 68368f8c..aaf1ae3a 100644
--- a/mhcflurry/class1_allele_specific_hyperparameters.py
+++ b/mhcflurry/class1_allele_specific_hyperparameters.py
@@ -13,7 +13,7 @@
# limitations under the License.
N_PRETRAIN_EPOCHS = 10
-N_EPOCHS = 100
+N_EPOCHS = 125
ACTIVATION = "relu"
INITIALIZATION_METHOD = "lecun_uniform"
EMBEDDING_DIM = 64
diff --git a/scripts/mhcflurry-class1-web-server.py b/scripts/mhcflurry-class1-web-server.py
index 3806eed5..0f6dca94 100755
--- a/scripts/mhcflurry-class1-web-server.py
+++ b/scripts/mhcflurry-class1-web-server.py
@@ -21,13 +21,13 @@ from __future__ import (
)
import argparse
-from bottle import post, request, run
+from bottle import post, request, run, get
from mhcflurry.common import (
split_uppercase_sequences,
split_allele_names,
)
-from mhcflurry.class1 import predict
+from mhcflurry.class1 import predict, supported_alleles
parser = argparse.ArgumentParser()
@@ -47,8 +47,17 @@ def get_binding_value():
return "ERROR: no allele given"
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)
+ return result_df.to_csv(sep="\t", index=False, float_format="%0.4f")
+
+@get('/alleles')
+def get_supported_alleles():
+ peptide_lengths = "8,9,10,11,12"
+ strings = [
+ "%s\t%s" % (allele, peptide_lengths)
+ for allele in supported_alleles()
+ ]
+ return "\n".join(strings)
if __name__ == "__main__":
args = parser.parse_args()
- run(host=args.host, port=args.port, debug=args.debug)
\ No newline at end of file
+ run(host=args.host, port=args.port, debug=args.debug)
--
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