├── .dockerignore ├── .github └── workflows │ ├── build-release.yml │ ├── changelog.yml │ ├── ci.yml │ ├── dependabot.yml │ ├── dockerpublish.yml │ ├── pythonpublish.yml │ └── test-build.yml ├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── assets ├── PyProphet_Logo.png ├── PyProphet_Logo_paths.svg └── PyProphet_Logo_transparent_bg.png ├── dist-scripts ├── create-manylinux.sh └── manylinux.patch ├── docs ├── Makefile ├── README.md ├── _static │ └── custom.css ├── api │ ├── config.rst │ ├── index.rst │ ├── io.rst │ ├── ipf.rst │ ├── levels_context.rst │ └── scoring.rst ├── cli.rst ├── conf.py ├── file_formats.rst ├── index.rst ├── templates │ └── class.rst └── user_guide │ ├── alignment_integration_workflow.rst │ ├── file_conversion.rst │ ├── index.rst │ └── pyprophet_workflow.rst ├── packaging └── pyinstaller │ ├── hooks │ ├── hook-duckdb.py │ ├── hook-pyopenms.py │ ├── hook-xgboost.py │ └── hook.pyprophet.py │ └── run_pyprophet.py ├── pyproject.toml ├── pyprophet ├── __init__.py ├── _base.py ├── _config.py ├── cli │ ├── __init__.py │ ├── export.py │ ├── ipf.py │ ├── levels_context.py │ ├── merge.py │ ├── score.py │ └── util.py ├── export │ ├── __init__.py │ ├── calibration_report.py │ ├── export_compound.py │ └── export_report.py ├── filter.py ├── glyco │ ├── __init__.py │ ├── export.py │ ├── glycoform.py │ ├── pepmass │ │ ├── __init__.py │ │ ├── glycomass.py │ │ ├── modmass.py │ │ └── pepmass.py │ ├── report.py │ ├── scoring.py │ └── stats.py ├── io │ ├── __init__.py │ ├── _base.py │ ├── dispatcher.py │ ├── export │ │ ├── __init__.py │ │ ├── osw.py │ │ ├── parquet.py │ │ ├── split_parquet.py │ │ └── sqmass.py │ ├── ipf │ │ ├── __init__.py │ │ ├── osw.py │ │ ├── parquet.py │ │ ├── split_parquet.py │ │ └── tsv.py │ ├── levels_context │ │ ├── __init__.py │ │ ├── osw.py │ │ ├── parquet.py │ │ └── split_parquet.py │ ├── scoring │ │ ├── __init__.py │ │ ├── osw.py │ │ ├── parquet.py │ │ ├── split_parquet.py │ │ └── tsv.py │ └── util.py ├── ipf.py ├── levels_contexts.py ├── main.py ├── report.py ├── scoring │ ├── __init__.py │ ├── _optimized.c │ ├── _optimized.pyx │ ├── classifiers.py │ ├── data_handling.py │ ├── optimized.py │ ├── pyprophet.py │ ├── runner.py │ └── semi_supervised.py ├── split.py ├── stats.py ├── util.py └── version_check.py ├── requirements.txt ├── sandbox ├── compare.py ├── compare_classifiers.py ├── compare_gauss_kernel_density_estimate.py ├── createFakeOSW.ipynb ├── dummyOSWScoredData.osw ├── export_parquet.py ├── fakeLib.tsv ├── generate_storey_ref_data.R ├── ludovic.py ├── p_values.txt ├── reproduce_r.sh ├── test_pyprophet_export_parquet.py ├── test_qvalue_ref_data.csv └── test_statsmodels_kde.py ├── scripts └── build │ ├── README.md │ ├── build_linux.sh │ ├── build_macos.sh │ ├── build_windows.bat │ ├── create_linux_packages.sh │ ├── create_macos_dmg.sh │ └── create_windows_installer.ps1 ├── setup.cfg ├── setup.py └── tests ├── .gitignore ├── Create_OSW_test.ipynb ├── README.md ├── __init__.py ├── _regtest_outputs ├── test_pyprophet_export.test_compound_0.out ├── test_pyprophet_export.test_compound_1.out ├── test_pyprophet_export.test_compound_ms1.out ├── test_pyprophet_export.test_compound_ms2.out ├── test_pyprophet_export.test_compound_unscored.out ├── test_pyprophet_export.test_feature_scores_ms1_ms2_transition.out ├── test_pyprophet_export.test_feature_scores_parquet_with_scores.out ├── test_pyprophet_export.test_feature_scores_scored_osw.out ├── test_pyprophet_export.test_feature_scores_split_parquet_with_scores.out ├── test_pyprophet_export.test_feature_scores_unscored_osw.out ├── test_pyprophet_export.test_ipf_0.out ├── test_pyprophet_export.test_ipf_1.out ├── test_pyprophet_export.test_ipf_2.out ├── test_pyprophet_export.test_ipf_3.out ├── test_pyprophet_export.test_ipf_analysis[False-augmented].out ├── test_pyprophet_export.test_ipf_analysis[False-disable].out ├── test_pyprophet_export.test_ipf_analysis[False-peptidoform].out ├── test_pyprophet_export.test_ipf_analysis[True-disable].out ├── test_pyprophet_export.test_osw_0.out ├── test_pyprophet_export.test_osw_1.out ├── test_pyprophet_export.test_osw_2.out ├── test_pyprophet_export.test_osw_3.out ├── test_pyprophet_export.test_osw_analysis[osw-False-False-False].out ├── test_pyprophet_export.test_osw_analysis[osw-False-False-True].out ├── test_pyprophet_export.test_osw_analysis[osw-False-True-False].out ├── test_pyprophet_export.test_osw_analysis[osw-True-False-False].out ├── test_pyprophet_export.test_osw_analysis[parquet-False-False-False].out ├── test_pyprophet_export.test_osw_analysis[parquet-False-False-True].out ├── test_pyprophet_export.test_osw_analysis[parquet-False-True-False].out ├── test_pyprophet_export.test_osw_analysis[parquet-True-False-False].out ├── test_pyprophet_export.test_osw_analysis[split_parquet-False-False-False].out ├── test_pyprophet_export.test_osw_analysis[split_parquet-False-False-True].out ├── test_pyprophet_export.test_osw_analysis[split_parquet-False-True-False].out ├── test_pyprophet_export.test_osw_analysis[split_parquet-True-False-False].out ├── test_pyprophet_export.test_osw_analysis_libExport[osw-False-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[osw-False-iRT].out ├── test_pyprophet_export.test_osw_analysis_libExport[osw-True-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[osw-True-iRT].out ├── test_pyprophet_export.test_osw_analysis_libExport[parquet-False-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[parquet-False-iRT].out ├── test_pyprophet_export.test_osw_analysis_libExport[parquet-True-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[parquet-True-iRT].out ├── test_pyprophet_export.test_osw_analysis_libExport[split_parquet-False-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[split_parquet-False-iRT].out ├── test_pyprophet_export.test_osw_analysis_libExport[split_parquet-True-RT].out ├── test_pyprophet_export.test_osw_analysis_libExport[split_parquet-True-iRT].out ├── test_pyprophet_export.test_osw_unscored.out ├── test_pyprophet_export.test_osw_unscored[osw].out ├── test_pyprophet_export.test_osw_unscored[parquet].out ├── test_pyprophet_export.test_osw_unscored[split_parquet].out ├── test_pyprophet_export.test_parquet_export_no_transition_data.out ├── test_pyprophet_export.test_parquet_export_scored_osw.out ├── test_pyprophet_export.test_parquet_export_split_format.out ├── test_pyprophet_export.test_parquet_export_with_ipf.out ├── test_pyprophet_export_parquet.test_osw_to_parquet_scoring_format_0.out ├── test_pyprophet_export_parquet.test_osw_to_parquet_scoring_format_1.out ├── test_pyprophet_export_parquet.test_osw_to_parquet_scoring_format_2.out ├── test_pyprophet_export_parquet.test_osw_to_parquet_scoring_format_3.out ├── test_pyprophet_ipf.test_ipf_0.out ├── test_pyprophet_ipf.test_ipf_1.out ├── test_pyprophet_ipf.test_ipf_2.out ├── test_pyprophet_ipf.test_ipf_3.out ├── test_pyprophet_ipf.test_ipf_4.out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_off-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_off-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_off-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_off-ms2_on-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_on-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_on-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_on-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[osw-h0_on-ms2_on-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_off-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_off-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_off-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_off-ms2_on-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_on-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_on-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_on-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[parquet-h0_on-ms2_on-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_off-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_off-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_off-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_off-ms2_on-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_on-ms2_off-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_on-ms2_off-ms1_on].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_on-ms2_on-ms1_off].out ├── test_pyprophet_ipf.test_ipf_scoring[split_parquet-h0_on-ms2_on-ms1_on].out ├── test_pyprophet_levels_contexts.test_ipf_1.out ├── test_pyprophet_levels_contexts.test_levels_contexts_0.out ├── test_pyprophet_levels_contexts.test_peptide_levels[osw-experiment-wide].out ├── test_pyprophet_levels_contexts.test_peptide_levels[osw-global].out ├── test_pyprophet_levels_contexts.test_peptide_levels[osw-run-specific].out ├── test_pyprophet_levels_contexts.test_peptide_levels[parquet-experiment-wide].out ├── test_pyprophet_levels_contexts.test_peptide_levels[parquet-global].out ├── test_pyprophet_levels_contexts.test_peptide_levels[parquet-run-specific].out ├── test_pyprophet_levels_contexts.test_peptide_levels[split_parquet-experiment-wide].out ├── test_pyprophet_levels_contexts.test_peptide_levels[split_parquet-global].out ├── test_pyprophet_levels_contexts.test_peptide_levels[split_parquet-run-specific].out ├── test_pyprophet_levels_contexts.test_protein_levels[osw-experiment-wide].out ├── test_pyprophet_levels_contexts.test_protein_levels[osw-global].out ├── test_pyprophet_levels_contexts.test_protein_levels[osw-run-specific].out ├── test_pyprophet_levels_contexts.test_protein_levels[parquet-experiment-wide].out ├── test_pyprophet_levels_contexts.test_protein_levels[parquet-global].out ├── test_pyprophet_levels_contexts.test_protein_levels[parquet-run-specific].out ├── test_pyprophet_levels_contexts.test_protein_levels[split_parquet-experiment-wide].out ├── test_pyprophet_levels_contexts.test_protein_levels[split_parquet-global].out ├── test_pyprophet_levels_contexts.test_protein_levels[split_parquet-run-specific].out ├── test_pyprophet_score.test_multi_split_parquet_0.out ├── test_pyprophet_score.test_multi_split_parquet_1.out ├── test_pyprophet_score.test_multi_split_parquet_2.out ├── test_pyprophet_score.test_multi_split_parquet_3.out ├── test_pyprophet_score.test_multi_split_parquet_6.out ├── test_pyprophet_score.test_multi_split_parquet_7.out ├── test_pyprophet_score.test_multi_split_parquet_8.out ├── test_pyprophet_score.test_multi_split_parquet_9.out ├── test_pyprophet_score.test_multi_split_parquet_apply_weights.out ├── test_pyprophet_score.test_multi_split_parquet_histgbc.out ├── test_pyprophet_score.test_osw_0.out ├── test_pyprophet_score.test_osw_1.out ├── test_pyprophet_score.test_osw_10.out ├── test_pyprophet_score.test_osw_2.out ├── test_pyprophet_score.test_osw_3.out ├── test_pyprophet_score.test_osw_4.out ├── test_pyprophet_score.test_osw_5.out ├── test_pyprophet_score.test_osw_6.out ├── test_pyprophet_score.test_osw_7.out ├── test_pyprophet_score.test_osw_8.out ├── test_pyprophet_score.test_osw_9.out ├── test_pyprophet_score.test_osw_histgbc.out ├── test_pyprophet_score.test_osw_histgbc_multilevel.out ├── test_pyprophet_score.test_osw_histgbc_tune.out ├── test_pyprophet_score.test_parquet_0.out ├── test_pyprophet_score.test_parquet_1.out ├── test_pyprophet_score.test_parquet_2.out ├── test_pyprophet_score.test_parquet_3.out ├── test_pyprophet_score.test_parquet_6.out ├── test_pyprophet_score.test_parquet_7.out ├── test_pyprophet_score.test_parquet_8.out ├── test_pyprophet_score.test_parquet_9.out ├── test_pyprophet_score.test_parquet_apply_weights.out ├── test_pyprophet_score.test_parquet_histgbc.out ├── test_pyprophet_score.test_parquet_histgbc_tune.out ├── test_pyprophet_score.test_split_parquet_0.out ├── test_pyprophet_score.test_split_parquet_1.out ├── test_pyprophet_score.test_split_parquet_2.out ├── test_pyprophet_score.test_split_parquet_3.out ├── test_pyprophet_score.test_split_parquet_6.out ├── test_pyprophet_score.test_split_parquet_7.out ├── test_pyprophet_score.test_split_parquet_8.out ├── test_pyprophet_score.test_split_parquet_9.out ├── test_pyprophet_score.test_split_parquet_apply_weights.out ├── test_pyprophet_score.test_split_parquet_histgbc.out ├── test_pyprophet_score.test_tsv_0.out ├── test_pyprophet_score.test_tsv_1.out ├── test_pyprophet_score.test_tsv_2.out ├── test_pyprophet_score.test_tsv_3.out ├── test_pyprophet_score.test_tsv_apply_weights.out ├── test_stats.test_lfdr.out ├── test_stats.test_qvalue.out ├── test_stats.test_random.out └── test_stats.test_stat_metrics.out ├── data ├── test_data.osw ├── test_data.oswpq │ ├── precursors_features.parquet │ └── transition_features.parquet ├── test_data.oswpqd │ └── napedro_L120420_010_SW.oswpq │ │ ├── precursors_features.parquet │ │ └── transition_features.parquet ├── test_data.parquet ├── test_data.txt ├── test_data_compound.osw ├── test_data_compound_ms1.tsv ├── test_data_compound_ms2.tsv ├── test_invalid_data.txt ├── test_lfdr_ref_data.csv └── test_qvalue_ref_data.csv ├── test.ipynb ├── test_data_handling.py ├── test_io_ipf.py ├── test_io_levels_contexts.py ├── test_io_scoring.py ├── test_ipf.py ├── test_optimized.py ├── test_pyprophet_export.py ├── test_pyprophet_ipf.py ├── test_pyprophet_levels_contexts.py ├── test_pyprophet_score.py ├── test_stats.py 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