Support NetMHCpan-4.1

This builds on work from @denklewer and @amitschang in #163 to support
NetMHCpan 4.1.

Author: timodonnell

mhctools/__init__.py

@@ -17,7 +17,8 @@
 from .netmhc_pan import NetMHCpan
 from .netmhc_pan28 import NetMHCpan28
 from .netmhc_pan3 import NetMHCpan3
-from .netmhc_pan4 import NetMHCpan4, NetMHCpan41, NetMHCpan4_BA, NetMHCpan4_EL
+from .netmhc_pan4 import NetMHCpan4, NetMHCpan4_BA, NetMHCpan4_EL
+from .netmhc_pan41 import NetMHCpan41, NetMHCpan41_BA, NetMHCpan41_EL
 from .netmhcii_pan import NetMHCIIpan, NetMHCIIpan3, NetMHCIIpan4, NetMHCIIpan4_BA, NetMHCIIpan4_EL
 from .random_predictor import RandomBindingPredictor
 from .unsupported_allele import UnsupportedAllele

mhctools/cli/args.py

@@ -34,6 +34,9 @@
     NetMHCpan4,
     NetMHCpan4_EL,
     NetMHCpan4_BA,
+    NetMHCpan41,
+    NetMHCpan41_EL,
+    NetMHCpan41_BA,
     NetMHCIIpan,
     NetMHCIIpan3,
     NetMHCIIpan4,
@@ -61,6 +64,9 @@
     "netmhcpan4": NetMHCpan4,
     "netmhcpan4-ba": NetMHCpan4_BA,
     "netmhcpan4-el": NetMHCpan4_EL,
+    "netmhcpan41": NetMHCpan41,
+    "netmhcpan41-ba": NetMHCpan41_BA,
+    "netmhcpan41-el": NetMHCpan41_EL,
     "netmhcpan28": NetMHCpan28,
     "netmhcpan3": NetMHCpan3,
     "netmhciipan": NetMHCIIpan,

mhctools/netmhc_pan.py

@@ -20,7 +20,7 @@
 from .netmhc_pan28 import NetMHCpan28
 from .netmhc_pan3 import NetMHCpan3
 from .netmhc_pan4 import NetMHCpan4
-
+from .netmhc_pan41 import NetMHCpan41
 
 logger = logging.getLogger(__name__)
 
@@ -52,13 +52,12 @@ def NetMHCpan(
     }
     if "NetMHCpan version 2.8" in output_str:
         return NetMHCpan28(**common_kwargs)
-
     elif "NetMHCpan version 3.0" in output_str:
         return NetMHCpan3(**common_kwargs)
-
     elif "NetMHCpan version 4.0" in output_str:
         return NetMHCpan4(**common_kwargs)
-
+    elif "NetMHCpan version 4.1" in output_str:
+            return NetMHCpan4(**common_kwargs)
     else:
         raise RuntimeError(
-            "This software expects NetMHCpan version 2.8, 3.0, or 4.0")
+            "This software expects NetMHCpan version 2.8, 3.0, or 4.0, or 4.1")

mhctools/netmhc_pan4.py

@@ -55,43 +55,6 @@ def __init__(
             extra_flags=flags + extra_flags,
             process_limit=process_limit)
 
-class NetMHCpan41(BaseCommandlinePredictor):
-    def __init__(
-            self,
-            alleles,
-            default_peptide_lengths=[9],
-            program_name="netMHCpan",
-            process_limit=-1,
-            mode="binding_affinity",
-            extra_flags=[]):
-        """
-        Wrapper for NetMHCpan4.1.
-
-        The mode argument should be one of "binding_affinity" (default) or
-        "elution_score".
-        """
-
-        # The -BA flag is required to predict binding affinity
-        if mode == "binding_affinity":
-            flags = ["-BA"]
-        elif mode == "elution_score":
-            flags = []
-        else:
-            raise ValueError("Unsupported mode", mode)
-
-        BaseCommandlinePredictor.__init__(
-            self,
-            program_name=program_name,
-            alleles=alleles,
-            default_peptide_lengths=default_peptide_lengths,
-            parse_output_fn=partial(parse_netmhcpan41_stdout, mode=mode),
-            supported_alleles_flag="-listMHC",
-            input_file_flag="-f",
-            length_flag="-l",
-            allele_flag="-a",
-            extra_flags=flags + extra_flags,
-            process_limit=process_limit)
-
 class NetMHCpan4_EL(NetMHCpan4):
     """
     Wrapper for NetMHCpan4 when the preferred mode is elution score

mhctools/netmhc_pan41.py

@@ -0,0 +1,98 @@
+# Copyright (c) 2016-2023. Mount Sinai School of Medicine
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import print_function, division, absolute_import
+
+from .base_commandline_predictor import BaseCommandlinePredictor
+from .parsing import parse_netmhc41_stdout
+from functools import partial
+
+
+class NetMHCpan41(BaseCommandlinePredictor):
+    def __init__(
+            self,
+            alleles,
+            default_peptide_lengths=[9],
+            program_name="netMHCpan",
+            process_limit=-1,
+            mode="binding_affinity",
+            extra_flags=[]):
+        """
+        Wrapper for NetMHCpan4.1.
+
+        The mode argument should be one of "binding_affinity" (default) or
+        "elution_score".
+        """
+
+        # The -BA flag is required to predict binding affinity
+        if mode == "binding_affinity":
+            flags = ["-BA"]
+        elif mode == "elution_score":
+            flags = []
+        else:
+            raise ValueError("Unsupported mode", mode)
+
+        BaseCommandlinePredictor.__init__(
+            self,
+            program_name=program_name,
+            alleles=alleles,
+            default_peptide_lengths=default_peptide_lengths,
+            parse_output_fn=partial(parse_netmhc41_stdout, mode=mode),
+            supported_alleles_flag="-listMHC",
+            input_file_flag="-f",
+            length_flag="-l",
+            allele_flag="-a",
+            extra_flags=flags + extra_flags,
+            process_limit=process_limit)
+
+class NetMHCpan41_EL(NetMHCpan41):
+    """
+    Wrapper for NetMHCpan4 when the preferred mode is elution score
+    """
+    def __init__(
+            self,
+            alleles,
+            default_peptide_lengths=[9],
+            program_name="netMHCpan",
+            process_limit=-1,
+            extra_flags=[]):
+        NetMHCpan41.__init__(
+            self,
+            alleles=alleles,
+            default_peptide_lengths=default_peptide_lengths,
+            program_name=program_name,
+            process_limit=process_limit,
+            mode="elution_score",
+            extra_flags=extra_flags)
+
+
+class NetMHCpan41_BA(NetMHCpan41):
+    """
+    Wrapper for NetMHCpan4 when the preferred mode is binding affinity
+    """
+    def __init__(
+            self,
+            alleles,
+            default_peptide_lengths=[9],
+            program_name="netMHCpan",
+            process_limit=-1,
+            extra_flags=[]):
+        NetMHCpan41.__init__(
+            self,
+            alleles=alleles,
+            default_peptide_lengths=default_peptide_lengths,
+            program_name=program_name,
+            process_limit=process_limit,
+            mode="binding_affinity",
+            extra_flags=extra_flags)

mhctools/parsing.py

@@ -285,6 +285,44 @@ def parse_netmhc4_stdout(
         rank_index=13,
         score_index=11)
 
+def parse_netmhc41_stdout(
+        stdout,
+        mode,
+        prediction_method_name="netmhc41",
+        sequence_key_mapping=None):
+    """
+    # NetMHCpan version 4.1b
+
+    # Tmpdir made /tmp/netMHCpanGjkOCb
+    # Input is in PEPTIDE format
+
+    # Make both EL and BA predictions
+
+    HLA-A02:01 : Distance to training data  0.000 (using nearest neighbor HLA-A02:01)
+
+    # Rank Threshold for Strong binding peptides   0.500
+    # Rank Threshold for Weak binding peptides   2.000
+    ---------------------------------------------------------------------------------------------------------------------------
+     Pos         MHC        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL Score_BA %Rank_BA  Aff(nM) BindLevel
+    ---------------------------------------------------------------------------------------------------------------------------
+       1 HLA-A*02:01       SIINFEKL SII-NFEKL  0  0  0  3  1     SIINFEKL         PEPLIST 0.0100620    6.723 0.110414   20.171 15140.42
+    ---------------------------------------------------------------------------------------------------------------------------
+
+    Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 0. Number of weak binders 0. Number of peptides 1
+    """
+    assert mode in ("binding_affinity", "elution_score")
+    return parse_stdout(
+        stdout=stdout,
+        prediction_method_name=prediction_method_name,
+        sequence_key_mapping=sequence_key_mapping,
+        key_index=10,
+        offset_index=0,
+        peptide_index=2,
+        allele_index=1,
+        ic50_index=15 if mode == "binding_affinity" else None,
+        rank_index=14 if mode == "binding_affinity" else 12,
+        score_index=13 if mode == "binding_affinity" else 11)
+
 def parse_netmhcpan28_stdout(
         stdout,
         prediction_method_name="netmhcpan",

test/test_netmhc_pan.py

@@ -23,6 +23,7 @@
     "netMHCpan-2.8",
     "netMHCpan-3.0",
     "netMHCpan-4.0",
+    "netMHCpan-4.1",
 ]