Merge pull request #1181 from ldhtnp/issue-457

Added argument for specifying NetMHCIIpan/NetMHCIIpanEL version
griffithlab · Feb 19, 2025 · 620b1df · 620b1df
2 parents 337358c + 49a4685
commit 620b1df
Show file tree

Hide file tree

Showing 41 changed files with 6,639 additions and 67 deletions.
diff --git a/docs/pvacbind/additional_commands.rst b/docs/pvacbind/additional_commands.rst
@@ -31,6 +31,11 @@ List Valid Algorithms
     :func: define_parser
     :prog: pvacbind valid_algorithms
 
+List Valid NetMHCIIpan/NetMHCIIpanEL Versions
+---------------------------------------------
+
+.. program-output:: pvacbind valid_netmhciipan_versions -h
+
 List Allele-Specific Cutoffs
 ----------------------------
 

diff --git a/docs/pvacbind/features.rst b/docs/pvacbind/features.rst
@@ -58,14 +58,14 @@ MHCflurry                                                 yes
 MHCnuggets                                                no
 ================================================= ======= ========================
 
-================================================== ======= ========================
-MHC Class II Binding Affinity Prediction Algorithm Version Supports Percentile Rank
-================================================== ======= ========================
-NetMHCIIpan                                        4.1     yes
-SMMalign                                           1.1     yes
-NNalign                                            2.3     yes
-MHCnuggets                                                 no
-================================================== ======= ========================
+================================================== ================================================================ ========================
+MHC Class II Binding Affinity Prediction Algorithm Version                                                          Supports Percentile Rank
+================================================== ================================================================ ========================
+NetMHCIIpan                                        4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+SMMalign                                           1.1                                                              yes
+NNalign                                            2.3                                                              yes
+MHCnuggets                                                                                                          no
+================================================== ================================================================ ========================
 
 ======================================== ======= ========================
 MHC Class I Elution Prediction Algorithm Version Supports Percentile Rank
@@ -76,11 +76,11 @@ MHCflurryEL                                      | Processing Score: no;
 BigMHC_EL                                        no
 ======================================== ======= ========================
 
-========================================= ======= ========================
-MHC Class II Elution Prediction Algorithm Version Supports Percentile Rank
-========================================= ======= ========================
-NetMHCIIpanEL                             4.1     yes
-========================================= ======= ========================
+========================================= ================================================================ ========================
+MHC Class II Elution Prediction Algorithm Version                                                          Supports Percentile Rank
+========================================= ================================================================ ========================
+NetMHCIIpan                               4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+========================================= ================================================================ ========================
 
 =============================================== ======= ========================
 MHC Class I Immunogenicity Prediction Algorithm Version Supports Percentile Rank

diff --git a/docs/pvacfuse/additional_commands.rst b/docs/pvacfuse/additional_commands.rst
@@ -41,6 +41,11 @@ List Valid Algorithms
     :func: define_parser
     :prog: pvacfuse valid_algorithms
 
+List Valid NetMHCIIpan/NetMHCIIpanEL Versions
+---------------------------------------------
+
+.. program-output:: pvacfuse valid_netmhciipan_versions -h
+
 List Allele-Specific Cutoffs
 ----------------------------
 

diff --git a/docs/pvacfuse/features.rst b/docs/pvacfuse/features.rst
@@ -62,14 +62,14 @@ MHCflurry                                                 yes
 MHCnuggets                                                no
 ================================================= ======= ========================
 
-================================================== ======= ========================
-MHC Class II Binding Affinity Prediction Algorithm Version Supports Percentile Rank
-================================================== ======= ========================
-NetMHCIIpan                                        4.1     yes
-SMMalign                                           1.1     yes
-NNalign                                            2.3     yes
-MHCnuggets                                                 no
-================================================== ======= ========================
+================================================== ================================================================ ========================
+MHC Class II Binding Affinity Prediction Algorithm Version                                                          Supports Percentile Rank
+================================================== ================================================================ ========================
+NetMHCIIpan                                        4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+SMMalign                                           1.1                                                              yes
+NNalign                                            2.3                                                              yes
+MHCnuggets                                                                                                          no
+================================================== ================================================================ ========================
 
 ======================================== ======= ========================
 MHC Class I Elution Prediction Algorithm Version Supports Percentile Rank
@@ -80,11 +80,11 @@ MHCflurryEL                                      | Processing Score: no;
 BigMHC_EL                                        no
 ======================================== ======= ========================
 
-========================================= ======= ========================
-MHC Class II Elution Prediction Algorithm Version Supports Percentile Rank
-========================================= ======= ========================
-NetMHCIIpanEL                             4.1     yes
-========================================= ======= ========================
+========================================= ================================================================ ========================
+MHC Class II Elution Prediction Algorithm Version                                                          Supports Percentile Rank
+========================================= ================================================================ ========================
+NetMHCIIpan                               4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+========================================= ================================================================ ========================
 
 =============================================== ======= ========================
 MHC Class I Immunogenicity Prediction Algorithm Version Supports Percentile Rank

diff --git a/docs/pvacseq/additional_commands.rst b/docs/pvacseq/additional_commands.rst
@@ -55,6 +55,11 @@ List Valid Algorithms
     :func: define_parser
     :prog: pvacseq valid_algorithms
 
+List Valid NetMHCIIpan/NetMHCIIpanEL Versions
+---------------------------------------------
+
+.. program-output:: pvacseq valid_netmhciipan_versions -h
+
 List Allele-Specific Cutoffs
 ----------------------------
 

diff --git a/docs/pvacseq/features.rst b/docs/pvacseq/features.rst
@@ -66,14 +66,14 @@ MHCflurry                                                 yes
 MHCnuggets                                                no
 ================================================= ======= ========================
 
-================================================== ======= ========================
-MHC Class II Binding Affinity Prediction Algorithm Version Supports Percentile Rank
-================================================== ======= ========================
-NetMHCIIpan                                        4.1     yes
-SMMalign                                           1.1     yes
-NNalign                                            2.3     yes
-MHCnuggets                                                 no
-================================================== ======= ========================
+================================================== ================================================================ ========================
+MHC Class II Binding Affinity Prediction Algorithm Version                                                          Supports Percentile Rank
+================================================== ================================================================ ========================
+NetMHCIIpan                                        4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+SMMalign                                           1.1                                                              yes
+NNalign                                            2.3                                                              yes
+MHCnuggets                                                                                                          no
+================================================== ================================================================ ========================
 
 ======================================== ======= ========================
 MHC Class I Elution Prediction Algorithm Version Supports Percentile Rank
@@ -84,11 +84,11 @@ MHCflurryEL                                      | Processing Score: no;
 BigMHC_EL                                        no
 ======================================== ======= ========================
 
-========================================= ======= ========================
-MHC Class II Elution Prediction Algorithm Version Supports Percentile Rank
-========================================= ======= ========================
-NetMHCIIpanEL                             4.1     yes
-========================================= ======= ========================
+========================================= ================================================================ ========================
+MHC Class II Elution Prediction Algorithm Version                                                          Supports Percentile Rank
+========================================= ================================================================ ========================
+NetMHCIIpan                               4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+========================================= ================================================================ ========================
 
 =============================================== ======= ========================
 MHC Class I Immunogenicity Prediction Algorithm Version Supports Percentile Rank

diff --git a/docs/pvacsplice/additional_commands.rst b/docs/pvacsplice/additional_commands.rst
@@ -22,6 +22,11 @@ List Valid Alleles
 
 .. program-output:: pvacsplice valid_alleles -h
 
+List Valid NetMHCIIpan/NetMHCIIpanEL Versions
+---------------------------------------------
+
+.. program-output:: pvacsplice valid_netmhciipan_versions -h
+
 List Allele-Specific Cutoffs
 ----------------------------
 

diff --git a/docs/pvacsplice/features.rst b/docs/pvacsplice/features.rst
@@ -64,14 +64,14 @@ MHCflurry                                                 yes
 MHCnuggets                                                no
 ================================================= ======= ========================
 
-================================================== ======= ========================
-MHC Class II Binding Affinity Prediction Algorithm Version Supports Percentile Rank
-================================================== ======= ========================
-NetMHCIIpan                                        4.1     yes
-SMMalign                                           1.1     yes
-NNalign                                            2.3     yes
-MHCnuggets                                                 no
-================================================== ======= ========================
+================================================== ================================================================ ========================
+MHC Class II Binding Affinity Prediction Algorithm Version                                                          Supports Percentile Rank
+================================================== ================================================================ ========================
+NetMHCIIpan                                        4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+SMMalign                                           1.1                                                              yes
+NNalign                                            2.3                                                              yes
+MHCnuggets                                                                                                          no
+================================================== ================================================================ ========================
 
 ======================================== ======= ========================
 MHC Class I Elution Prediction Algorithm Version Supports Percentile Rank
@@ -82,11 +82,11 @@ MHCflurryEL                                      | Processing Score: no;
 BigMHC_EL                                        no
 ======================================== ======= ========================
 
-========================================= ======= ========================
-MHC Class II Elution Prediction Algorithm Version Supports Percentile Rank
-========================================= ======= ========================
-NetMHCIIpanEL                             4.1     yes
-========================================= ======= ========================
+========================================= ================================================================ ========================
+MHC Class II Elution Prediction Algorithm Version                                                          Supports Percentile Rank
+========================================= ================================================================ ========================
+NetMHCIIpan                               4.0 (not supported by standalone IEDB), 4.1 (default), 4.2., 4.3 yes
+========================================= ================================================================ ========================
 
 =============================================== ======= ========================
 MHC Class I Immunogenicity Prediction Algorithm Version Supports Percentile Rank

diff --git a/docs/pvacvector/additional_commands.rst b/docs/pvacvector/additional_commands.rst
@@ -53,6 +53,11 @@ List Valid Algorithms
     :func: define_parser
     :prog: pvacvector valid_algorithms
 
+List Valid NetMHCIIpan/NetMHCIIpanEL Versions
+---------------------------------------------
+
+.. program-output:: pvacvector valid_netmhciipan_versions -h
+
 List Allele-Specific Cutoffs
 ----------------------------
 

diff --git a/pvactools/lib/__init__.py b/pvactools/lib/__init__.py
@@ -12,6 +12,7 @@
     "output_parser",
     "valid_alleles",
     'valid_algorithms',
+    'valid_netmhciipan_versions',
     'net_chop',
     "netmhc_stab",
     "filter",