LICENSE
README.md
pyproject.toml
requirements.txt
tests/__init__.py
tests/common.py
tests/data.py
tests/test_args_outputs.py
tests/test_cached_predictor.py
tests/test_cli_cached_predictor.py
tests/test_cli_coverage.py
tests/test_cli_protein_changes.py
tests/test_cli_ranking.py
tests/test_cli_script.py
tests/test_contains_mutant_residues.py
tests/test_coverage_gaps.py
tests/test_dataframe.py
tests/test_deploy_script.py
tests/test_direct_input_regressions.py
tests/test_dsl_extensions.py
tests/test_dsl_polish.py
tests/test_dsl_roundtrip.py
tests/test_edge_case_fixtures.py
tests/test_effect_expression_filters.py
tests/test_end_to_end.py
tests/test_epitopes_from_commandline_args.py
tests/test_expression_integration.py
tests/test_expression_loader.py
tests/test_frameshift_fragments.py
tests/test_inputs.py
tests/test_integration.py
tests/test_io.py
tests/test_io_lens.py
tests/test_load_cufflinks_fpkm.py
tests/test_load_stringtie_gtf_fpkm.py
tests/test_mutant_epitope_predictions_class1.py
tests/test_mutant_epitope_predictions_class2.py
tests/test_padding.py
tests/test_peptide_mutation_interval.py
tests/test_predict_from_fragments.py
tests/test_predict_from_variants_refactor.py
tests/test_predictor_internals.py
tests/test_protein_fragment.py
tests/test_ranking.py
tests/test_result.py
tests/test_rna_helpers.py
tests/test_self_proteome.py
tests/test_sequence_helpers.py
tests/test_sources.py
tests/test_sources_optional.py
tests/test_validation_and_edge_cases.py
tests/test_variant_expression_filters.py
tests/test_wide.py
topiary/__init__.py
topiary/cached.py
topiary/filters.py
topiary/inputs.py
topiary/io.py
topiary/io_lens.py
topiary/io_protein_fragment.py
topiary/predictor.py
topiary/properties.py
topiary/protein_fragment.py
topiary/result.py
topiary/self_proteome.py
topiary/sequence_helpers.py
topiary/sources.py
topiary/wide.py
topiary.egg-info/PKG-INFO
topiary.egg-info/SOURCES.txt
topiary.egg-info/dependency_links.txt
topiary.egg-info/entry_points.txt
topiary.egg-info/requires.txt
topiary.egg-info/top_level.txt
topiary/cli/__init__.py
topiary/cli/args.py
topiary/cli/cached_predictor.py
topiary/cli/errors.py
topiary/cli/filtering.py
topiary/cli/outputs.py
topiary/cli/protein_changes.py
topiary/cli/rna.py
topiary/cli/script.py
topiary/cli/sequence.py
topiary/ranking/__init__.py
topiary/ranking/apply.py
topiary/ranking/nodes.py
topiary/ranking/parser.py
topiary/rna/__init__.py
topiary/rna/common.py
topiary/rna/cufflinks.py
topiary/rna/expression_loader.py
topiary/rna/gtf.py