add get URL for alleles

mhcflurry/class1.py

 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

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

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)