Adding ability to run mhctools with netMHCpan 4.0.

Also: adding support for easily running with multiple versions of the same netMHC tool (same original binary name, optionally different versioned binary names made by the user) installed on one machine.

mhctools/cli/args.py

@@ -31,6 +31,7 @@
     NetMHCpan,
     NetMHCpan28,
     NetMHCpan3,
+    NetMHCpan4,
     NetMHCIIpan,
     NetMHCcons,
     RandomBindingPredictor,
@@ -52,6 +53,7 @@
     "netmhcpan": NetMHCpan,
     "netmhcpan28": NetMHCpan28,
     "netmhcpan3": NetMHCpan3,
+    "netmhcpan4": NetMHCpan4,
     "netmhciipan": NetMHCIIpan,
     "netmhccons": NetMHCcons,
     "random": RandomBindingPredictor,
@@ -71,6 +73,15 @@
     "mhcflurry": MHCflurry,
 }
 
+# The versioned program names will be tried first, and if they don't exist in the path, we'll
+# fall back to the standard install program names.
+versioned_mhc_predictor_program_names = {
+    "netmhcpan28": ["netMHCpan-2.8", "netMHCpan"],
+    "netmhcpan3": ["netMHCpan-3.0", "netMHCpan"],
+    "netmhcpan4": ["netMHCpan-4.0", "netMHCpan"],
+    "netmhc3": ["netMHC-3.4", "netMHC"],
+}
+
 def add_mhc_args(arg_parser):
     mhc_options_arg_group = arg_parser.add_argument_group(
         title="MHC Prediction Options",
@@ -92,11 +103,6 @@ def add_mhc_args(arg_parser):
         type=parse_int_list,
         help="Lengths of epitopes to consider for MHC binding prediction")
 
-    mhc_options_arg_group.add_argument(
-        "--mhc-epitope-lengths",
-        type=parse_int_list,
-        help="Deprecated name for --mhc-peptide-lengths")
-
     mhc_options_arg_group.add_argument(
         "--mhc-alleles-file",
         help="File with one HLA allele per line")
@@ -139,8 +145,6 @@ def mhc_binding_predictor_from_args(args):
             "Invalid MHC prediction method: %s" % (args.mhc_predictor,))
     alleles = mhc_alleles_from_args(args)
     peptide_lengths = args.mhc_peptide_lengths
-    if not peptide_lengths:
-        peptide_lengths = args.mhc_epitope_lengths
     logger.info(
         ("Building MHC binding prediction %s"
          " for alleles %s"
@@ -153,4 +157,19 @@ def mhc_binding_predictor_from_args(args):
         kwargs["default_peptide_lengths"] = peptide_lengths
     if args.mhc_predictor_models_path:
         kwargs["models_path"] = args.mhc_predictor_models_path
-    return mhc_class(**kwargs)
+
+    # support optionally installed program names here, like netMHCpan-3.0 instead of
+    # netMHCpan - will make it possible to run different versions of the same netMHC suite tools
+    # in the same environment for comparison
+    program_names = versioned_mhc_predictor_program_names.get(args.mhc_predictor)
+    if program_names is None:
+        return mhc_class(**kwargs)
+
+    for program_name in program_names:
+        try:
+            predictor = mhc_class(program_name=program_name, **kwargs)
+            return predictor
+        except FileNotFoundError:
+            continue
+
+    raise ValueError("Cannot create MHC binding predictor from kwargs %s" % kwargs)