fixed commandline script for making predictions

mhcflurry/common.py

@@ -20,8 +20,7 @@ from collections import defaultdict
 import numpy as np
 
 def parse_int_list(s):
-    return [int(part.strip() for part in s.split(","))]
-
+    return [int(part.strip()) for part in s.split(",")]
 
 def split_uppercase_sequences(s):
     return [part.strip().upper() for part in s.split(",")]

script/mhcflurry-predict-class1.py

@@ -28,6 +28,7 @@ from mhcflurry.common import (
     split_allele_names,
 )
 from mhcflurry.predict import predict
+from six import string_types
 
 parser = argparse.ArgumentParser()
 
@@ -55,5 +56,19 @@ parser.add_argument(
 
 if __name__ == "__main__":
     args = parser.parse_args()
-    df = predict(alleles=args.mhc, peptides=args.sequence)
+    if len(args.peptide_lengths) == 0:
+        raise ValueError("Must specify at least one peptide length")
+
+    long_sequences = args.sequence
+    if isinstance(long_sequences, string_types):
+        long_sequences = [long_sequences]
+
+    peptides = []
+    for peptide_length in args.peptide_lengths:
+        for long_sequence in long_sequences:
+            total_length = len(long_sequence)
+            for i in range(total_length - peptide_length):
+                peptides.append(long_sequence[i:i + peptide_length])
+    print("Running predictor over %d sub-sequences" % len(peptides))
+    df = predict(alleles=args.mhc, peptides=peptides)
     print(df.to_csv(sep="\t", index=False), end="")