diff --git a/docs/pvacbind/filter_commands.rst b/docs/pvacbind/filter_commands.rst index d0872cbde..72e588f5e 100644 --- a/docs/pvacbind/filter_commands.rst +++ b/docs/pvacbind/filter_commands.rst @@ -48,7 +48,7 @@ prediction's HLA allele are used instead of the value set via the ``--binding-th For HLA alleles where no allele-specific binding threshold is available, the binding threshold is used as a fallback. Alleles with allele-specific threshold as well as the value of those thresholds can be printed by executing -the ``pvacbind allele_specific_cutoffs`` command. +the ``pvactools allele_specific_cutoffs`` command. In addition to being able to filter on the IC50 score columns, the binding filter also offers the ability to filter on the percentile score using the diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst index 663fb62a4..4a8b16677 100644 --- a/docs/pvacbind/output_files.rst +++ b/docs/pvacbind/output_files.rst @@ -237,7 +237,7 @@ provided to the pVACfuse run: allele-specific binding thresholds. For alleles where no allele-specific binding threshold is available, use the ``--binding-threshold`` as a fallback. To print a list of alleles that have - specific binding thresholds and the value of those thresholds, run ``pvacfuse allele_specific_cutoffs``. + specific binding thresholds and the value of those thresholds, run ``pvactools allele_specific_cutoffs``. - False * - ``--binding-percentile-threshold`` - Use this threshold to filter epitopes on the IC50 %ile MT score. diff --git a/docs/pvacfuse/filter_commands.rst b/docs/pvacfuse/filter_commands.rst index 6d4f6fd6c..2d8823285 100644 --- a/docs/pvacfuse/filter_commands.rst +++ b/docs/pvacfuse/filter_commands.rst @@ -47,7 +47,7 @@ prediction's HLA allele are used instead of the value set via the ``--binding-th For HLA alleles where no allele-specific binding threshold is available, the binding threshold is used as a fallback. Alleles with allele-specific threshold as well as the value of those thresholds can be printed by executing -the ``pvacfuse allele_specific_cutoffs`` command. +the ``pvactools allele_specific_cutoffs`` command. In addition to being able to filter on the IC50 score columns, the binding filter also offers the ability to filter on the percentile score using the diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst index 9a57bebe6..0ddde15e6 100644 --- a/docs/pvacfuse/output_files.rst +++ b/docs/pvacfuse/output_files.rst @@ -275,7 +275,7 @@ provided to the pVACfuse run: allele-specific binding thresholds. For alleles where no allele-specific binding threshold is available, use the ``--binding-threshold`` as a fallback. To print a list of alleles that have - specific binding thresholds and the value of those thresholds, run ``pvacfuse allele_specific_cutoffs``. + specific binding thresholds and the value of those thresholds, run ``pvactools allele_specific_cutoffs``. - False * - ``--binding-percentile-threshold`` - Use this threshold to filter epitopes on the IC50 %ile MT score. diff --git a/docs/pvacseq/filter_commands.rst b/docs/pvacseq/filter_commands.rst index 5388bbc1c..22bca31d7 100644 --- a/docs/pvacseq/filter_commands.rst +++ b/docs/pvacseq/filter_commands.rst @@ -56,7 +56,7 @@ prediction's HLA allele are used instead of the value set via the ``--binding-th For HLA alleles where no allele-specific binding threshold is available, the binding threshold is used as a fallback. Alleles with allele-specific threshold as well as the value of those thresholds can be printed by executing -the ``pvacseq allele_specific_cutoffs`` command. +the ``pvactools allele_specific_cutoffs`` command. The binding filter also offers the option to filter on ``Fold Change`` columns, which contain the ratio of the MT score to the WT Score. This option can be activated by setting the @@ -189,7 +189,7 @@ prediction's HLA allele are used instead of the value set via the ``--binding-th For HLA alleles where no allele-specific binding threshold is available, the binding threshold is used as a fallback. Alleles with allele-specific threshold as well as the value of those thresholds can be printed by executing -the ``pvacseq allele_specific_cutoffs`` command. +the ``pvactools allele_specific_cutoffs`` command. **Additional Considerations** diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst index 57d4e4530..bf7b1ba56 100644 --- a/docs/pvacseq/output_files.rst +++ b/docs/pvacseq/output_files.rst @@ -489,7 +489,7 @@ To tier the Best Peptide, several cutoffs can be adjusted using arguments provid allele-specific binding thresholds. For alleles where no allele-specific binding threshold is available, use the ``--binding-threshold`` as a fallback. To print a list of alleles that have - specific binding thresholds and the value of those thresholds, run ``pvacseq allele_specific_cutoffs``. + specific binding thresholds and the value of those thresholds, run ``pvactools allele_specific_cutoffs``. - False * - ``--binding-percentile-threshold`` - Use this threshold to filter epitopes on the IC50 %ile MT score. diff --git a/docs/pvacsplice/filter_commands.rst b/docs/pvacsplice/filter_commands.rst index 05631da2e..01877de9a 100644 --- a/docs/pvacsplice/filter_commands.rst +++ b/docs/pvacsplice/filter_commands.rst @@ -52,7 +52,7 @@ prediction's HLA allele are used instead of the value set via the ``--binding-th For HLA alleles where no allele-specific binding threshold is available, the binding threshold is used as a fallback. Alleles with allele-specific threshold as well as the value of those thresholds can be printed by executing -the ``pvacsplice allele_specific_cutoffs`` command. +the ``pvactools allele_specific_cutoffs`` command. In addition to being able to filter on the IC50 score columns, the binding filter also offers the ability to filter on the percentile score using the diff --git a/docs/pvacsplice/output_files.rst b/docs/pvacsplice/output_files.rst index 10ffaf9b4..488be48bd 100644 --- a/docs/pvacsplice/output_files.rst +++ b/docs/pvacsplice/output_files.rst @@ -384,7 +384,7 @@ To tier the Best Peptide, several cutoffs can be adjusted using arguments provid allele-specific binding thresholds. For alleles where no allele-specific binding threshold is available, use the ``--binding-threshold`` as a fallback. To print a list of alleles that have - specific binding thresholds and the value of those thresholds, run ``pvacseq allele_specific_cutoffs``. + specific binding thresholds and the value of those thresholds, run ``pvactools allele_specific_cutoffs``. - False * - ``--binding-percentile-threshold`` - Use this threshold to filter epitopes on the IC50 %ile MT score. diff --git a/pvactools/lib/binding_filter.py b/pvactools/lib/binding_filter.py index 5f1087f7e..9d1cab75a 100644 --- a/pvactools/lib/binding_filter.py +++ b/pvactools/lib/binding_filter.py @@ -155,7 +155,7 @@ def parser(cls, tool): ) parser.add_argument( '-a', '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `%s allele_specific_cutoffs`. " % tool + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/lib/run_argument_parser.py b/pvactools/lib/run_argument_parser.py index 759adde81..ebda4f647 100644 --- a/pvactools/lib/run_argument_parser.py +++ b/pvactools/lib/run_argument_parser.py @@ -139,7 +139,7 @@ def binding_args(self, tool_name): ) self.parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `%s allele_specific_cutoffs`. " % tool_name + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', @@ -606,7 +606,7 @@ def __init__(self): ) self.parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds when evaluating junctional epitopes. To print the allele-specific binding thresholds run `pvacvector allele_specific_cutoffs`. " + help="Use allele-specific binding thresholds when evaluating junctional epitopes. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/lib/update_tiers.py b/pvactools/lib/update_tiers.py index f5d3e302a..d69d48787 100644 --- a/pvactools/lib/update_tiers.py +++ b/pvactools/lib/update_tiers.py @@ -76,7 +76,7 @@ def parser(cls, tool): ) parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds when evaluating the binding criteria for tiering. To print the allele-specific binding thresholds run `%s allele_specific_cutoffs`. " % tool + help="Use allele-specific binding thresholds when evaluating the binding criteria for tiering. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/tools/pvacbind/generate_aggregated_report.py b/pvactools/tools/pvacbind/generate_aggregated_report.py index 0f2f5d7b6..6fa20717a 100644 --- a/pvactools/tools/pvacbind/generate_aggregated_report.py +++ b/pvactools/tools/pvacbind/generate_aggregated_report.py @@ -28,7 +28,7 @@ def define_parser(): ) parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvacbind allele_specific_cutoffs`. " + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/tools/pvacfuse/generate_aggregated_report.py b/pvactools/tools/pvacfuse/generate_aggregated_report.py index 0d0709b47..d5df83546 100644 --- a/pvactools/tools/pvacfuse/generate_aggregated_report.py +++ b/pvactools/tools/pvacfuse/generate_aggregated_report.py @@ -28,7 +28,7 @@ def define_parser(): ) parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvacfuse allele_specific_cutoffs`. " + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/tools/pvacseq/generate_aggregated_report.py b/pvactools/tools/pvacseq/generate_aggregated_report.py index 5e932ada7..f4c0eaf3a 100644 --- a/pvactools/tools/pvacseq/generate_aggregated_report.py +++ b/pvactools/tools/pvacseq/generate_aggregated_report.py @@ -32,7 +32,7 @@ def define_parser(): ) parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvacseq allele_specific_cutoffs`. " + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true', diff --git a/pvactools/tools/pvacsplice/generate_aggregated_report.py b/pvactools/tools/pvacsplice/generate_aggregated_report.py index d3936c173..8db51e481 100644 --- a/pvactools/tools/pvacsplice/generate_aggregated_report.py +++ b/pvactools/tools/pvacsplice/generate_aggregated_report.py @@ -32,7 +32,7 @@ def define_parser(): ) parser.add_argument( '--allele-specific-binding-thresholds', - help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvacseq allele_specific_cutoffs`. " + help="Use allele-specific binding thresholds. To print the allele-specific binding thresholds run `pvactools allele_specific_cutoffs`. " + "If an allele does not have a special threshold value, the `--binding-threshold` value will be used.", default=False, action='store_true',