allow commas in peptide and allele strings for mhcflurry-predict, incrememented keras version

mhcflurry/predict_command.py

@@ -122,8 +122,19 @@ def run(argv=sys.argv[1:]):
             parser.error(
                 "Specify either an input CSV file or both the "
                 "--alleles and --peptides arguments")
-
-        pairs = list(itertools.product(args.alleles, args.peptides))
+        # split user specified allele and peptide strings in case they
+        # contain multiple entries separated by commas
+        alleles = []
+        for allele_string in args.alleles:
+            alleles.extend([s.strip() for s in allele_string.split(",")])
+        peptides = []
+        for peptide in args.peptides:
+            peptides.extend(peptide.strip() for p in peptide.split(","))
+        for peptide in peptides:
+            if not peptide.isalpha():
+                raise ValueError(
+                    "Unexpected character(s) in peptide '%s'" % peptide)
+        pairs = list(itertools.product(alleles, peptides))
         df = pandas.DataFrame({
             "allele": [p[0] for p in pairs],
             "peptide": [p[1] for p in pairs],

requirements.txt

@@ -2,7 +2,7 @@ numpy>= 1.11
 pandas>=0.13.1
 appdirs
 theano>=0.8.2
-keras==1.1.0
+keras==1.2.0
 fancyimpute>=0.0.12
 scikit-learn
 h5py

setup.py

@@ -53,7 +53,7 @@ if __name__ == '__main__':
         'pandas>=0.13.1',
         'appdirs',
         'theano>=0.8.2',
-        'keras==1.1.0',
+        'keras==1.2.0',
         'fancyimpute>=0.0.12',
         'scikit-learn',
         'h5py',