From c3c1d898ca9f2434307ad4350c471f0bc88ac2ea Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Wed, 15 May 2024 13:01:48 -0500
Subject: [PATCH 01/10] Add new R dependencies for pVACview

---
 pvactools/tools/pvacview/Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pvactools/tools/pvacview/Dockerfile b/pvactools/tools/pvacview/Dockerfile
index bb05b8fc..7ec96c13 100644
--- a/pvactools/tools/pvacview/Dockerfile
+++ b/pvactools/tools/pvacview/Dockerfile
@@ -18,7 +18,9 @@ RUN R -e "install.packages(c('shiny',\
   'shinydashboardPlus', \
   'shinycssloaders', \
   'fresh', \
-  'RCurl' ), repos='https://cran.rstudio.com/')"
+  'RCurl', \
+  'shinyWidgets', \
+  'colourpicker'), repos='https://cran.rstudio.com/')"
 
 RUN R -e "devtools::install_github('eclarke/ggbeeswarm', ref='v0.6.1')"
 

From 6cbb2ac4ced341b7321a944a258193d3ac32fc1c Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Wed, 15 May 2024 13:02:14 -0500
Subject: [PATCH 02/10] Add 4.2 releases page

---
 docs/releases.rst     |  1 +
 docs/releases/4_2.rst | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)
 create mode 100644 docs/releases/4_2.rst

diff --git a/docs/releases.rst b/docs/releases.rst
index bb443c13..fb33f8e4 100644
--- a/docs/releases.rst
+++ b/docs/releases.rst
@@ -17,3 +17,4 @@ Release Notes
    releases/3_1
    releases/4_0
    releases/4_1
+   releases/4_2
diff --git a/docs/releases/4_2.rst b/docs/releases/4_2.rst
new file mode 100644
index 00000000..de193ebd
--- /dev/null
+++ b/docs/releases/4_2.rst
@@ -0,0 +1,19 @@
+Version 4.2
+===========
+
+Version 4.2.0
+-------------
+
+This is a minor feature release. It adds the following features:
+
+- We added two new modules to pVACview: a :ref:`neofox_module` to visualize
+  NeoFox neoantigen annotations and a :ref:`custom_module` to visualize
+  neoantigen data in a TSV file, for example output files from VaxRank,
+  NeoPredPipe, or antigen.garnish.2.
+- We added a :ref:`vignette <pvacseq_vignette>` to our documentation to provide
+  an extended tutorial on how evaluate neoantigen candidates using pVACview.
+
+This release also fixes the following bug(s):
+
+- When running pVACfuse with Arriba input data, the 3' transcript was not
+  being parsed correctly. This release fixes this issue.

From a34c86393e9b895602dbda8e0a433340cf26473c Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Tue, 4 Jun 2024 14:07:54 -0500
Subject: [PATCH 03/10] added valid_algorithms.py to each tool and lib

---
 pvactools/lib/valid_algorithms.py             | 55 +++++++++++++++++++
 pvactools/tools/pvacbind/valid_algorithms.py  | 15 +++++
 pvactools/tools/pvacfuse/valid_algorithms.py  | 15 +++++
 pvactools/tools/pvacseq/valid_algorithms.py   | 15 +++++
 .../tools/pvacvector/valid_algorithms.py      | 15 +++++
 5 files changed, 115 insertions(+)
 create mode 100644 pvactools/lib/valid_algorithms.py
 create mode 100644 pvactools/tools/pvacbind/valid_algorithms.py
 create mode 100644 pvactools/tools/pvacfuse/valid_algorithms.py
 create mode 100644 pvactools/tools/pvacseq/valid_algorithms.py
 create mode 100644 pvactools/tools/pvacvector/valid_algorithms.py

diff --git a/pvactools/lib/valid_algorithms.py b/pvactools/lib/valid_algorithms.py
new file mode 100644
index 00000000..96bcf4b8
--- /dev/null
+++ b/pvactools/lib/valid_algorithms.py
@@ -0,0 +1,55 @@
+import sys
+import argparse
+
+from pvactools.lib.prediction_class import *
+
+class ValidAlgorithms:
+    def __init__(self, allele, species):
+        self.allele = allele
+        self.species = species
+
+    def print_valid_algorithms(self):
+        if self.allele is None:
+            valid_algorithms = []
+            if self.species is None:
+                valid_algorithms = PredictionClass.prediction_methods()
+            else:
+                prediction_algorithms = PredictionClass.prediction_methods()
+                for algorithm in prediction_algorithms:
+                    cls = globals()[algorithm]
+                    alleles = cls().valid_allele_names()
+                    for allele in alleles:
+                        if cls.species_for_allele(allele) == self.species:
+                            valid_algorithms.append(algorithm)
+                            break
+        else:
+            valid_algorithms = []
+            PredictionClass.check_alleles_valid([self.allele])
+            prediction_algorithms = PredictionClass.prediction_methods()
+            for algorithm in prediction_algorithms:
+                cls = globals()[algorithm]
+                alleles = cls().valid_allele_names()
+                if (self.allele in alleles) \
+                      and (PredictionClass.species_for_allele(self.allele) == self.species \
+                           or self.species == None):
+                    valid_algorithms.append(algorithm)
+        print(', '.join([a for a in valid_algorithms]))
+
+    @classmethod
+    def parser(cls, tool="pvacseq"):
+        parser = argparse.ArgumentParser(
+            "%s valid_algorithms" % tool,
+            description="Show a list of algorithms supported given the specified species and/or allele",
+            formatter_class=argparse.ArgumentDefaultsHelpFormatter
+        )
+        parser.add_argument(
+            "-a", "--allele",
+            help="Name of the allele to use to get supported algorithms. "
+                 + "For a list of available alleles, use: `{} valid_alleles`.".format(tool),
+        )
+        parser.add_argument(
+            "-s", "--species",
+            choices=sorted(set(list(PredictionClass.allele_to_species_map().values())), key=str.casefold),
+            help="Show valid algorithms for the selected species only",
+        )
+        return parser
diff --git a/pvactools/tools/pvacbind/valid_algorithms.py b/pvactools/tools/pvacbind/valid_algorithms.py
new file mode 100644
index 00000000..ef6b3798
--- /dev/null
+++ b/pvactools/tools/pvacbind/valid_algorithms.py
@@ -0,0 +1,15 @@
+import sys
+
+from pvactools.lib.valid_algorithms import ValidAlgorithms
+
+def define_parser():
+    return ValidAlgorithms.parser('pvacbind')
+
+def main(args_input = sys.argv[1:]):
+    parser = define_parser()
+    args = parser.parse_args(args_input)
+
+    ValidAlgorithms(args.allele, args.species).print_valid_algorithms()
+
+if __name__ == "__main__":
+    main()
diff --git a/pvactools/tools/pvacfuse/valid_algorithms.py b/pvactools/tools/pvacfuse/valid_algorithms.py
new file mode 100644
index 00000000..e29974b5
--- /dev/null
+++ b/pvactools/tools/pvacfuse/valid_algorithms.py
@@ -0,0 +1,15 @@
+import sys
+
+from pvactools.lib.valid_algorithms import ValidAlgorithms
+
+def define_parser():
+    return ValidAlgorithms.parser('pvacfuse')
+
+def main(args_input = sys.argv[1:]):
+    parser = define_parser()
+    args = parser.parse_args(args_input)
+
+    ValidAlgorithms(args.allele, args.species).print_valid_algorithms()
+
+if __name__ == "__main__":
+    main()
diff --git a/pvactools/tools/pvacseq/valid_algorithms.py b/pvactools/tools/pvacseq/valid_algorithms.py
new file mode 100644
index 00000000..81dea467
--- /dev/null
+++ b/pvactools/tools/pvacseq/valid_algorithms.py
@@ -0,0 +1,15 @@
+import sys
+
+from pvactools.lib.valid_algorithms import ValidAlgorithms
+
+def define_parser():
+    return ValidAlgorithms.parser('pvacseq')
+
+def main(args_input = sys.argv[1:]):
+    parser = define_parser()
+    args = parser.parse_args(args_input)
+
+    ValidAlgorithms(args.allele, args.species).print_valid_algorithms()
+
+if __name__ == "__main__":
+    main()
diff --git a/pvactools/tools/pvacvector/valid_algorithms.py b/pvactools/tools/pvacvector/valid_algorithms.py
new file mode 100644
index 00000000..dd6aa902
--- /dev/null
+++ b/pvactools/tools/pvacvector/valid_algorithms.py
@@ -0,0 +1,15 @@
+import sys
+
+from pvactools.lib.valid_algorithms import ValidAlgorithms
+
+def define_parser():
+    return ValidAlgorithms.parser('pvacvector')
+
+def main(args_input = sys.argv[1:]):
+    parser = define_parser()
+    args = parser.parse_args(args_input)
+
+    ValidAlgorithms(args.allele, args.species).print_valid_algorithms()
+
+if __name__ == "__main__":
+    main()

From 1c05b14d7ab2dfefe59c4a98aabda4de53c50310 Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Tue, 4 Jun 2024 14:28:14 -0500
Subject: [PATCH 04/10] updated documentation with valid algorithms command
 info

---
 docs/pvacbind/additional_commands.rst   | 12 ++++++++++++
 docs/pvacfuse/additional_commands.rst   | 12 ++++++++++++
 docs/pvacseq/additional_commands.rst    | 12 ++++++++++++
 docs/pvacvector/additional_commands.rst | 12 ++++++++++++
 4 files changed, 48 insertions(+)

diff --git a/docs/pvacbind/additional_commands.rst b/docs/pvacbind/additional_commands.rst
index 11299335..470adf87 100644
--- a/docs/pvacbind/additional_commands.rst
+++ b/docs/pvacbind/additional_commands.rst
@@ -19,6 +19,18 @@ List Valid Alleles
 
 .. program-output:: pvacbind valid_alleles -h
 
+.. _valid_algorithms:
+
+List Valid Algorithms
+------------------
+
+.. program-output:: pvacbind valid_algorithms -h
+
+.. .. argparse::
+    :module: lib.valid_algorithms
+    :func: define_parser
+    :prog: pvacbind valid_algorithms
+
 List Allele-Specific Cutoffs
 ----------------------------
 
diff --git a/docs/pvacfuse/additional_commands.rst b/docs/pvacfuse/additional_commands.rst
index b9a35ad0..9944b972 100644
--- a/docs/pvacfuse/additional_commands.rst
+++ b/docs/pvacfuse/additional_commands.rst
@@ -29,6 +29,18 @@ List Valid Alleles
     :func: define_parser
     :prog: pvacfuse valid_alleles
 
+.. _valid_algorithms:
+
+List Valid Algorithms
+------------------
+
+.. program-output:: pvacfuse valid_algorithms -h
+
+.. .. argparse::
+    :module: lib.valid_algorithms
+    :func: define_parser
+    :prog: pvacfuse valid_algorithms
+
 List Allele-Specific Cutoffs
 ----------------------------
 
diff --git a/docs/pvacseq/additional_commands.rst b/docs/pvacseq/additional_commands.rst
index 782240fd..05cec6ec 100644
--- a/docs/pvacseq/additional_commands.rst
+++ b/docs/pvacseq/additional_commands.rst
@@ -43,6 +43,18 @@ List Valid Alleles
     :func: define_parser
     :prog: pvacseq valid_alleles
 
+.. _valid_algorithms:
+
+List Valid Algorithms
+------------------
+
+.. program-output:: pvacseq valid_algorithms -h
+
+.. .. argparse::
+    :module: lib.valid_algorithms
+    :func: define_parser
+    :prog: pvacseq valid_algorithms
+
 List Allele-Specific Cutoffs
 ----------------------------
 
diff --git a/docs/pvacvector/additional_commands.rst b/docs/pvacvector/additional_commands.rst
index 2aec1ea8..7d48a265 100644
--- a/docs/pvacvector/additional_commands.rst
+++ b/docs/pvacvector/additional_commands.rst
@@ -41,6 +41,18 @@ List Valid Alleles
     :func: define_parser
     :prog: pvacfuse valid_alleles
 
+.. _valid_algorithms:
+
+List Valid Algorithms
+------------------
+
+.. program-output:: pvacvector valid_algorithms -h
+
+.. .. argparse::
+    :module: lib.valid_algorithms
+    :func: define_parser
+    :prog: pvacvector valid_algorithms
+
 List Allele-Specific Cutoffs
 ----------------------------
 

From 4e8419905cd8e81ed3a009656e1d7055be803604 Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Tue, 4 Jun 2024 14:29:15 -0500
Subject: [PATCH 05/10] updated init files

---
 pvactools/lib/__init__.py              | 1 +
 pvactools/tools/pvacbind/__init__.py   | 1 +
 pvactools/tools/pvacfuse/__init__.py   | 1 +
 pvactools/tools/pvacseq/__init__.py    | 1 +
 pvactools/tools/pvacvector/__init__.py | 1 +
 5 files changed, 5 insertions(+)

diff --git a/pvactools/lib/__init__.py b/pvactools/lib/__init__.py
index 6fa426e9..152cfe8d 100644
--- a/pvactools/lib/__init__.py
+++ b/pvactools/lib/__init__.py
@@ -11,6 +11,7 @@
     "fasta_generator",
     "output_parser",
     "valid_alleles",
+    'valid_algorithms',
     'net_chop',
     "netmhc_stab",
     "filter",
diff --git a/pvactools/tools/pvacbind/__init__.py b/pvactools/tools/pvacbind/__init__.py
index 6f39e45e..e6623e1d 100644
--- a/pvactools/tools/pvacbind/__init__.py
+++ b/pvactools/tools/pvacbind/__init__.py
@@ -2,6 +2,7 @@
     'run',
     'binding_filter',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
     'top_score_filter',
diff --git a/pvactools/tools/pvacfuse/__init__.py b/pvactools/tools/pvacfuse/__init__.py
index 54b6775c..87dd312e 100644
--- a/pvactools/tools/pvacfuse/__init__.py
+++ b/pvactools/tools/pvacfuse/__init__.py
@@ -3,6 +3,7 @@
     'binding_filter',
     'coverage_filter',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
     'top_score_filter',
diff --git a/pvactools/tools/pvacseq/__init__.py b/pvactools/tools/pvacseq/__init__.py
index 1bac38f5..f59e3d1a 100644
--- a/pvactools/tools/pvacseq/__init__.py
+++ b/pvactools/tools/pvacseq/__init__.py
@@ -2,6 +2,7 @@
     'run',
     'binding_filter',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
     'coverage_filter',
diff --git a/pvactools/tools/pvacvector/__init__.py b/pvactools/tools/pvacvector/__init__.py
index 96edab08..a068c830 100644
--- a/pvactools/tools/pvacvector/__init__.py
+++ b/pvactools/tools/pvacvector/__init__.py
@@ -2,6 +2,7 @@
     'run',
     'visualize',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
 ]

From ba42e17b898be3c48e6bed84d6e154b0a666b3c0 Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Tue, 4 Jun 2024 14:29:48 -0500
Subject: [PATCH 06/10] updated main.py files for new command

---
 pvactools/tools/pvacbind/main.py   | 7 +++++++
 pvactools/tools/pvacfuse/main.py   | 7 +++++++
 pvactools/tools/pvacseq/main.py    | 7 +++++++
 pvactools/tools/pvacvector/main.py | 7 +++++++
 4 files changed, 28 insertions(+)

diff --git a/pvactools/tools/pvacbind/main.py b/pvactools/tools/pvacbind/main.py
index 5a38b86c..d6463a50 100644
--- a/pvactools/tools/pvacbind/main.py
+++ b/pvactools/tools/pvacbind/main.py
@@ -81,6 +81,13 @@ def main():
     )
     valid_alleles_parser.set_defaults(func=valid_alleles)
 
+    valid_algorithms_parser = subparsers.add_parser(
+        "valid_algorithms",
+        help="Show a list of algorithms supported given the specified species and/or allele",
+        add_help=False
+    )
+    valid_algorithms_parser.set_defaults(func=valid_algorithms)
+
     allele_specific_cutoffs_parser = subparsers.add_parser(
         "allele_specific_cutoffs",
         help="Show the allele specific cutoffs",
diff --git a/pvactools/tools/pvacfuse/main.py b/pvactools/tools/pvacfuse/main.py
index 759a2467..6d571917 100644
--- a/pvactools/tools/pvacfuse/main.py
+++ b/pvactools/tools/pvacfuse/main.py
@@ -79,6 +79,13 @@ def define_parser():
     )
     valid_alleles_parser.set_defaults(func=valid_alleles)
 
+    valid_algorithms_parser = subparsers.add_parser(
+        "valid_algorithms",
+        help="Show a list of algorithms supported given the specified species and/or allele",
+        add_help=False
+    )
+    valid_algorithms_parser.set_defaults(func=valid_algorithms)
+
     identify_problematic_amino_acids_parser = subparsers.add_parser(
         "identify_problematic_amino_acids",
         help="Mark problematic amino acid positions in each epitope or filter entries that have problematic amino acids.",
diff --git a/pvactools/tools/pvacseq/main.py b/pvactools/tools/pvacseq/main.py
index 1d0fc659..0ebf3e5b 100644
--- a/pvactools/tools/pvacseq/main.py
+++ b/pvactools/tools/pvacseq/main.py
@@ -108,6 +108,13 @@ def define_parser():
     )
     valid_alleles_parser.set_defaults(func=valid_alleles)
 
+    valid_algorithms_parser = subparsers.add_parser(
+        "valid_algorithms",
+        help="Show a list of algorithms supported given the specified species and/or allele",
+        add_help=False
+    )
+    valid_algorithms_parser.set_defaults(func=valid_algorithms)
+
     allele_specific_cutoffs_parser = subparsers.add_parser(
         "allele_specific_cutoffs",
         help="Show the allele specific cutoffs.",
diff --git a/pvactools/tools/pvacvector/main.py b/pvactools/tools/pvacvector/main.py
index 53073fa4..f5634289 100644
--- a/pvactools/tools/pvacvector/main.py
+++ b/pvactools/tools/pvacvector/main.py
@@ -28,6 +28,13 @@ def define_parser():
     )
     valid_alleles_parser.set_defaults(func=valid_alleles)
 
+    valid_algorithms_parser = subparsers.add_parser(
+        "valid_algorithms",
+        help="Show a list of algorithms supported given the specified species and/or allele",
+        add_help=False
+    )
+    valid_algorithms_parser.set_defaults(func=valid_algorithms)
+
     allele_specific_cutoffs_parser = subparsers.add_parser(
         "allele_specific_cutoffs",
         help="Show the allele specific cutoffs",

From 9841e5af6bd18bdefbd911e6fa26a15c94a3a27c Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Tue, 4 Jun 2024 14:30:51 -0500
Subject: [PATCH 07/10] added tests for valid algorithms command

---
 tests/test_pvacbind.py   | 14 ++++++++++++++
 tests/test_pvacfuse.py   | 14 ++++++++++++++
 tests/test_pvacseq.py    | 14 ++++++++++++++
 tests/test_pvacvector.py | 14 ++++++++++++++
 4 files changed, 56 insertions(+)

diff --git a/tests/test_pvacbind.py b/tests/test_pvacbind.py
index 6b980e9c..aaef4edc 100644
--- a/tests/test_pvacbind.py
+++ b/tests/test_pvacbind.py
@@ -68,6 +68,7 @@ def test_pvacbind_commands(self):
             "run",
             'binding_filter',
             'valid_alleles',
+            'valid_algorithms',
             'allele_specific_cutoffs',
             'download_example_data',
             "net_chop",
@@ -363,3 +364,16 @@ def test_pvacbind_combine_and_condense_steps(self):
                 output_file   = os.path.join(output_dir.name, 'combined', file_name)
                 expected_file = os.path.join(self.test_data_directory, 'combine_and_condense', 'combined', file_name)
                 self.assertTrue(compare(output_file, expected_file))
+    
+    def test_valid_algorithms_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pvactools_directory,
+            'pvactools',
+            "tools",
+            "pvacbind",
+            "valid_algorithms.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_valid_algorithms_runs(self):
+        valid_algorithms.main("")
diff --git a/tests/test_pvacfuse.py b/tests/test_pvacfuse.py
index c7f84d25..6a43e6a1 100644
--- a/tests/test_pvacfuse.py
+++ b/tests/test_pvacfuse.py
@@ -64,6 +64,7 @@ def test_pvacfuse_commands(self):
             "binding_filter",
             "coverage_filter",
             "valid_alleles",
+            "valid_algorithms",
             "download_example_data",
             "net_chop",
             "netmhc_stab",
@@ -205,6 +206,19 @@ def test_valid_alleles_compiles(self):
 
     def test_valid_alleles_runs(self):
         valid_alleles.main(["-p", "SMM"])
+    
+    def test_valid_algorithms_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pvactools_directory,
+            'pvactools',
+            "tools",
+            "pvacfuse",
+            "valid_algorithms.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_valid_algorithms_runs(self):
+        valid_algorithms.main("")
 
     def test_pvacfuse_pipeline(self):
         with patch('requests.post', unittest.mock.Mock(side_effect = lambda url, data, files=None: make_response(
diff --git a/tests/test_pvacseq.py b/tests/test_pvacseq.py
index 9764b2cf..3b197df4 100644
--- a/tests/test_pvacseq.py
+++ b/tests/test_pvacseq.py
@@ -82,6 +82,7 @@ def test_pvacseq_commands(self):
             "top_score_filter",
             "transcript_support_level_filter",
             "valid_alleles",
+            "valid_algorithms",
             'identify_problematic_amino_acids',
             ]:
             result = subprocess_run([
@@ -247,6 +248,19 @@ def test_valid_alleles_compiles(self):
 
     def test_valid_alleles_runs(self):
         valid_alleles.main(["-p", "SMM"])
+    
+    def test_valid_algorithms_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pvactools_directory,
+            'pvactools',
+            "tools",
+            "pvacseq",
+            "valid_algorithms.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_valid_algorithms_runs(self):
+        valid_algorithms.main("")
 
     def test_identify_problematic_amino_acids_compiles(self):
         compiled_run_path = py_compile.compile(os.path.join(
diff --git a/tests/test_pvacvector.py b/tests/test_pvacvector.py
index 49be7008..7ef50627 100644
--- a/tests/test_pvacvector.py
+++ b/tests/test_pvacvector.py
@@ -81,6 +81,7 @@ def test_pvacvector_commands(self):
             "run",
             "visualize",
             "valid_alleles",
+            "valid_algorithms",
             "allele_specific_cutoffs",
             "download_example_data",
             ]:
@@ -156,6 +157,19 @@ def test_valid_alleles_compiles(self):
 
     def test_valid_alleles_runs(self):
         valid_alleles.main(["-p", "SMM"])
+    
+    def test_valid_algorithms_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pvactools_directory,
+            'pvactools',
+            "tools",
+            "pvacvector",
+            "valid_algorithms.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_valid_algorithms_runs(self):
+        valid_algorithms.main("")
 
     def test_pvacvector_fa_input_runs_and_produces_expected_output(self):
         with patch('requests.post', unittest.mock.Mock(side_effect = lambda url, data: make_response(

From 062380d8a1231e9e6bea874705bb3a5dc029af12 Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Wed, 5 Jun 2024 10:33:05 -0500
Subject: [PATCH 08/10] fixed error in pvacvector tests

---
 tests/test_pvacvector.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_pvacvector.py b/tests/test_pvacvector.py
index 7ef50627..dffc9581 100644
--- a/tests/test_pvacvector.py
+++ b/tests/test_pvacvector.py
@@ -160,7 +160,7 @@ def test_valid_alleles_runs(self):
     
     def test_valid_algorithms_compiles(self):
         compiled_run_path = py_compile.compile(os.path.join(
-            self.pvactools_directory,
+            self.base_dir,
             'pvactools',
             "tools",
             "pvacvector",

From 95ddcbb6611b3a5d4a55d97804776ce2aa07b871 Mon Sep 17 00:00:00 2001
From: ldhtnp <ldhtnp@umsystem.edu>
Date: Wed, 5 Jun 2024 11:54:32 -0500
Subject: [PATCH 09/10] added species and allele compatibility check

---
 pvactools/lib/valid_algorithms.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pvactools/lib/valid_algorithms.py b/pvactools/lib/valid_algorithms.py
index 96bcf4b8..9a368663 100644
--- a/pvactools/lib/valid_algorithms.py
+++ b/pvactools/lib/valid_algorithms.py
@@ -23,8 +23,11 @@ def print_valid_algorithms(self):
                             valid_algorithms.append(algorithm)
                             break
         else:
-            valid_algorithms = []
             PredictionClass.check_alleles_valid([self.allele])
+            if (self.species != None and PredictionClass.species_for_allele(self.allele) != self.species):
+                print("Given species does not have that allele.")
+                return
+            valid_algorithms = []
             prediction_algorithms = PredictionClass.prediction_methods()
             for algorithm in prediction_algorithms:
                 cls = globals()[algorithm]

From cb2d395dea8f91d6a97e9e31cadca2c5eac966f1 Mon Sep 17 00:00:00 2001
From: Luke Hendrickson <64616402+ldhtnp@users.noreply.github.com>
Date: Wed, 5 Jun 2024 13:53:22 -0500
Subject: [PATCH 10/10] applied suggestions from the PR review

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>
---
 docs/pvacbind/additional_commands.rst   | 2 +-
 docs/pvacfuse/additional_commands.rst   | 2 +-
 docs/pvacseq/additional_commands.rst    | 2 +-
 docs/pvacvector/additional_commands.rst | 2 +-
 pvactools/lib/valid_algorithms.py       | 6 +++---
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/pvacbind/additional_commands.rst b/docs/pvacbind/additional_commands.rst
index 470adf87..5937691d 100644
--- a/docs/pvacbind/additional_commands.rst
+++ b/docs/pvacbind/additional_commands.rst
@@ -22,7 +22,7 @@ List Valid Alleles
 .. _valid_algorithms:
 
 List Valid Algorithms
-------------------
+---------------------
 
 .. program-output:: pvacbind valid_algorithms -h
 
diff --git a/docs/pvacfuse/additional_commands.rst b/docs/pvacfuse/additional_commands.rst
index 9944b972..f469f29f 100644
--- a/docs/pvacfuse/additional_commands.rst
+++ b/docs/pvacfuse/additional_commands.rst
@@ -32,7 +32,7 @@ List Valid Alleles
 .. _valid_algorithms:
 
 List Valid Algorithms
-------------------
+---------------------
 
 .. program-output:: pvacfuse valid_algorithms -h
 
diff --git a/docs/pvacseq/additional_commands.rst b/docs/pvacseq/additional_commands.rst
index 05cec6ec..5e01ca2e 100644
--- a/docs/pvacseq/additional_commands.rst
+++ b/docs/pvacseq/additional_commands.rst
@@ -46,7 +46,7 @@ List Valid Alleles
 .. _valid_algorithms:
 
 List Valid Algorithms
-------------------
+---------------------
 
 .. program-output:: pvacseq valid_algorithms -h
 
diff --git a/docs/pvacvector/additional_commands.rst b/docs/pvacvector/additional_commands.rst
index 7d48a265..2f975b9e 100644
--- a/docs/pvacvector/additional_commands.rst
+++ b/docs/pvacvector/additional_commands.rst
@@ -44,7 +44,7 @@ List Valid Alleles
 .. _valid_algorithms:
 
 List Valid Algorithms
-------------------
+---------------------
 
 .. program-output:: pvacvector valid_algorithms -h
 
diff --git a/pvactools/lib/valid_algorithms.py b/pvactools/lib/valid_algorithms.py
index 9a368663..c4731fb8 100644
--- a/pvactools/lib/valid_algorithms.py
+++ b/pvactools/lib/valid_algorithms.py
@@ -25,7 +25,7 @@ def print_valid_algorithms(self):
         else:
             PredictionClass.check_alleles_valid([self.allele])
             if (self.species != None and PredictionClass.species_for_allele(self.allele) != self.species):
-                print("Given species does not have that allele.")
+                raise Exception("Given species does not match given allele.")
                 return
             valid_algorithms = []
             prediction_algorithms = PredictionClass.prediction_methods()
@@ -36,7 +36,7 @@ def print_valid_algorithms(self):
                       and (PredictionClass.species_for_allele(self.allele) == self.species \
                            or self.species == None):
                     valid_algorithms.append(algorithm)
-        print(', '.join([a for a in valid_algorithms]))
+        print('\n'.join([a for a in valid_algorithms]))
 
     @classmethod
     def parser(cls, tool="pvacseq"):
@@ -47,7 +47,7 @@ def parser(cls, tool="pvacseq"):
         )
         parser.add_argument(
             "-a", "--allele",
-            help="Name of the allele to use to get supported algorithms. "
+            help="Show valid algorithms for the selected allele. "
                  + "For a list of available alleles, use: `{} valid_alleles`.".format(tool),
         )
         parser.add_argument(