Added new valid_algorithms command (#1106)

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
 ----------------------------
 

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
 ----------------------------
 

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
 ----------------------------
 

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
 ----------------------------
 

docs/releases.rst

@@ -17,3 +17,4 @@ Release Notes
    releases/3_1
    releases/4_0
    releases/4_1
+   releases/4_2

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.

pvactools/lib/__init__.py

@@ -11,6 +11,7 @@
     "fasta_generator",
     "output_parser",
     "valid_alleles",
+    'valid_algorithms',
     'net_chop',
     "netmhc_stab",
     "filter",

pvactools/lib/valid_algorithms.py

@@ -0,0 +1,58 @@
+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:
+            PredictionClass.check_alleles_valid([self.allele])
+            if (self.species != None and PredictionClass.species_for_allele(self.allele) != self.species):
+                raise Exception("Given species does not match given allele.")
+                return
+            valid_algorithms = []
+            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('\n'.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="Show valid algorithms for the selected allele. "
+                 + "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

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',

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",

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()

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',

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.",

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()

pvactools/tools/pvacseq/__init__.py

@@ -2,6 +2,7 @@
     'run',
     'binding_filter',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
     'coverage_filter',

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.",

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()

pvactools/tools/pvacvector/__init__.py

@@ -2,6 +2,7 @@
     'run',
     'visualize',
     'valid_alleles',
+    'valid_algorithms',
     'allele_specific_cutoffs',
     'download_example_data',
 ]

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",

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()

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')"
 

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("")

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(