NetMHCpan-4.1 support

[denklewer]

According to issue #152 parser does not support NetMHCpan-4.1
Here are the changes needed for NetMHCpan-4.1 support.
NetMHCpan-4.0 and NetMHCpan-4.1 have different column numbers in the std output.
So I made these changes based on NetMHCpan4 class.

[amitschang]

Is there any way to move this (or something similar) forward? I'm interested in using the tool for NetMHCpan4.1 and the output differences are a blocker, this seems to get things to work (at least in some cases), as long as it is combined with the following patch to ensure the write class and parser are used:

diff --git a/mhctools/netmhc_pan.py b/mhctools/netmhc_pan.py
index 8783791..7882da6 100644
--- a/mhctools/netmhc_pan.py
+++ b/mhctools/netmhc_pan.py
@@ -19,7 +19,7 @@ import os
 
 from .netmhc_pan28 import NetMHCpan28
 from .netmhc_pan3 import NetMHCpan3
-from .netmhc_pan4 import NetMHCpan4
+from .netmhc_pan4 import NetMHCpan4, NetMHCpan41
 
 
 logger = logging.getLogger(__name__)
@@ -59,6 +59,9 @@ def NetMHCpan(
     elif "NetMHCpan version 4.0" in output_str:
         return NetMHCpan4(**common_kwargs)
 
+    elif "NetMHCpan version 4.1" in output_str:
+        return NetMHCpan41(**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, 4.0, or 4.1")

If the original PR author is unavailable, happy to submit some changes. Many thanks!

[timodonnell]

Taking a look at this - thanks for contributing. I'm having trouble getting NetMHCpan-4.1 installed as the "Linux_x86_64/data" seems to be a symlink to nowhere in the currently distributed NetMHCpan-4.1b distribution. Could someone send me the contents of your "Linux_x86_64/data" directory in your NetMHCpan-4.1 installation?

[amitschang]

Thanks for looking! If it is useful, I have been utilizing the netmhcpan 4.1 installation packaged together in the griffithlab/pvactools:3.0.4-slim docker image, under /opt/iedb/mhc_i/method/netmhcpan-4.1-executable

[timodonnell]

Thank you! I was able to get the data from there.

…

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[timodonnell]

I just merged #165 which extends this PR with a few additional changes. On my end this seems to be working correctly with NetMHCpan 4.1. Can you confirm this works for you? Thanks for both of your help and patience