├── .bumpversion.toml ├── .github ├── ISSUE_TEMPLATE │ ├── bug-report.md │ └── feature_request.md ├── release.yml └── workflows │ ├── _run_tests.yml │ ├── branch-checks.yaml │ ├── bump_version.yml │ ├── code_review.yml │ ├── create_release.yml │ ├── pip_installation.yml │ └── publish_on_pypi.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── alpharaw ├── __init__.py ├── cli.py ├── dia │ └── normal_dia.py ├── ext │ ├── __init__.py │ ├── sciex │ │ ├── Clearcore2.Compression.dll │ │ ├── Clearcore2.Data.Acquisition.Client.dll │ │ ├── Clearcore2.Data.Acquisition.Contracts.dll │ │ ├── Clearcore2.Data.AnalystDataProvider.dll │ │ ├── Clearcore2.Data.Client.dll │ │ ├── Clearcore2.Data.Common.dll │ │ ├── Clearcore2.Data.CommonInterfaces.dll │ │ ├── Clearcore2.Data.Contracts.dll │ │ ├── Clearcore2.Data.Core.dll │ │ ├── Clearcore2.Data.Wiff2.dll │ │ ├── Clearcore2.Data.WiffReader.dll │ │ ├── Clearcore2.Data.dll │ │ ├── Clearcore2.DataService.dll │ │ ├── Clearcore2.Devices.Types.dll │ │ ├── Clearcore2.Domain.Acquisition.Methods.MassSpec.dll │ │ ├── Clearcore2.Domain.Acquisition.dll │ │ ├── Clearcore2.Infrastructure.dll │ │ ├── Clearcore2.InternalRawXYProcessing.dll │ │ ├── Clearcore2.Muni.dll │ │ ├── Clearcore2.RawXYProcessing.dll │ │ ├── Clearcore2.StructuredStorage.dll │ │ ├── Clearcore2.UserLog.Types.dll │ │ ├── Clearcore2.Utility.dll │ │ ├── Clearcore2.XmlHelpers.dll │ │ ├── Sciex.Clearcore.FMan.dll │ │ ├── Sciex.Data.Processing.dll │ │ ├── Sciex.Data.SimpleTypes.dll │ │ ├── Sciex.Data.XYData.dll │ │ ├── Sciex.FMan.dll │ │ ├── Sciex.Wiff.dll │ │ ├── SciexToolKit.dll │ │ ├── WiffOps4Python.dll │ │ └── protobuf-net.dll │ └── thermo_fisher │ │ ├── THERMO_LICENSE.txt │ │ ├── ThermoFisher.CommonCore.Data.dll │ │ └── ThermoFisher.CommonCore.RawFileReader.dll ├── feature │ ├── __init__.py │ ├── centroids.py │ ├── chem.py │ ├── finding.py │ ├── hills.py │ └── isotope_pattern.py ├── legacy_msdata │ ├── __init__.py │ └── mgf.py ├── match │ ├── __init__.py │ ├── mass_calibration.py │ ├── match_utils.py │ ├── psm_match.py │ ├── psm_match_alphatims.py │ └── spec_finder.py ├── ms_data_base.py ├── mzml.py ├── mzml_io │ ├── __init__.py │ ├── cv_constants.py │ └── mzml_writer.py ├── raw_access │ ├── __init__.py │ ├── clr_utils.py │ ├── pysciexwifffilereader.py │ └── pythermorawfilereader.py ├── resources │ ├── README.md │ └── psi-ms.owl ├── sciex.py ├── thermo.py ├── utils │ ├── __init__.py │ ├── centroiding.py │ ├── df_processing.py │ ├── ms_path_utils.py │ └── timstof.py ├── viz │ ├── __init__.py │ ├── df_utils.py │ ├── plot_utils.py │ ├── psm_plot.py │ ├── xic_plot.py │ └── xic_plot_tims.py └── wrappers │ ├── __init__.py │ ├── alphapept_wrapper.py │ └── alphatims_wrapper.py ├── docs ├── Makefile ├── build_docs.sh ├── conf.py ├── index.rst ├── match │ ├── match_utils.rst │ ├── psm_match.rst │ └── spec_finder.rst ├── match_modules.rst ├── reader_modules.rst ├── readers │ ├── mgf.rst │ ├── ms_data_base.rst │ ├── mzml.rst │ ├── sciex.rst │ └── thermo.rst ├── tutorials.rst ├── tutorials │ ├── base_settings.ipynb │ ├── ms_methods.ipynb │ ├── raw_readers.ipynb │ └── spectrum_peak_df_connection.png ├── viz │ ├── df_utils.rst │ ├── plot_utils.rst │ ├── psm_plot.rst │ └── xic_plot.rst └── viz_modules.rst ├── misc ├── CLA.md └── pip_install.sh ├── nbs ├── alpharaw_to_alphapept.ipynb ├── psm_match_alphatims.ipynb ├── test_dia_matching.ipynb ├── test_tims_match.ipynb └── test_viz.ipynb ├── nbs_tests ├── feature_finding.ipynb ├── legacy_msdata │ ├── mgf.ipynb │ └── mzml.ipynb ├── match │ ├── match_utils.ipynb │ └── psm_match.ipynb ├── test_alphatims_wrapper.ipynb ├── test_data │ └── small.pwiz.1.1.mzML ├── test_viz_multinotch.ipynb └── wrappers │ └── alphatims_wrapper.ipynb ├── pyproject.toml ├── release └── common │ └── build_wheel.sh ├── requirements ├── requirements.txt ├── requirements_development.txt ├── requirements_docs.txt ├── requirements_loose.txt ├── requirements_tests.txt └── requirements_viz.txt ├── ruff-lint-strict.toml └── tests ├── download_test_data.py ├── run_tests.sh └── unit ├── test_mzml_writer.py ├── test_remove_unused_peaks.py └── test_requirements.py /.bumpversion.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.bumpversion.toml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug-report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/ISSUE_TEMPLATE/bug-report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/release.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/release.yml -------------------------------------------------------------------------------- /.github/workflows/_run_tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/_run_tests.yml -------------------------------------------------------------------------------- /.github/workflows/branch-checks.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/branch-checks.yaml -------------------------------------------------------------------------------- /.github/workflows/bump_version.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/bump_version.yml -------------------------------------------------------------------------------- /.github/workflows/code_review.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/code_review.yml -------------------------------------------------------------------------------- /.github/workflows/create_release.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/create_release.yml -------------------------------------------------------------------------------- /.github/workflows/pip_installation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/pip_installation.yml -------------------------------------------------------------------------------- /.github/workflows/publish_on_pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.github/workflows/publish_on_pypi.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/README.md -------------------------------------------------------------------------------- /alpharaw/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/__init__.py -------------------------------------------------------------------------------- /alpharaw/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/cli.py -------------------------------------------------------------------------------- /alpharaw/dia/normal_dia.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/dia/normal_dia.py -------------------------------------------------------------------------------- /alpharaw/ext/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Compression.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Compression.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Acquisition.Client.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Acquisition.Client.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Acquisition.Contracts.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Acquisition.Contracts.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.AnalystDataProvider.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.AnalystDataProvider.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Client.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Client.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Common.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Common.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.CommonInterfaces.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.CommonInterfaces.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Contracts.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Contracts.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Core.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Core.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.Wiff2.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.Wiff2.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.WiffReader.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.WiffReader.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Data.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Data.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.DataService.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.DataService.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Devices.Types.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Devices.Types.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Domain.Acquisition.Methods.MassSpec.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Domain.Acquisition.Methods.MassSpec.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Domain.Acquisition.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Domain.Acquisition.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Infrastructure.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Infrastructure.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.InternalRawXYProcessing.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.InternalRawXYProcessing.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Muni.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Muni.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.RawXYProcessing.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.RawXYProcessing.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.StructuredStorage.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.StructuredStorage.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.UserLog.Types.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.UserLog.Types.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.Utility.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.Utility.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Clearcore2.XmlHelpers.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Clearcore2.XmlHelpers.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.Clearcore.FMan.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.Clearcore.FMan.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.Data.Processing.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.Data.Processing.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.Data.SimpleTypes.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.Data.SimpleTypes.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.Data.XYData.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.Data.XYData.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.FMan.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.FMan.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/Sciex.Wiff.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/Sciex.Wiff.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/SciexToolKit.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/SciexToolKit.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/WiffOps4Python.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/WiffOps4Python.dll -------------------------------------------------------------------------------- /alpharaw/ext/sciex/protobuf-net.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/sciex/protobuf-net.dll -------------------------------------------------------------------------------- /alpharaw/ext/thermo_fisher/THERMO_LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/thermo_fisher/THERMO_LICENSE.txt -------------------------------------------------------------------------------- /alpharaw/ext/thermo_fisher/ThermoFisher.CommonCore.Data.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/thermo_fisher/ThermoFisher.CommonCore.Data.dll -------------------------------------------------------------------------------- /alpharaw/ext/thermo_fisher/ThermoFisher.CommonCore.RawFileReader.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ext/thermo_fisher/ThermoFisher.CommonCore.RawFileReader.dll -------------------------------------------------------------------------------- /alpharaw/feature/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/feature/centroids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/feature/centroids.py -------------------------------------------------------------------------------- /alpharaw/feature/chem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/feature/chem.py -------------------------------------------------------------------------------- /alpharaw/feature/finding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/feature/finding.py -------------------------------------------------------------------------------- /alpharaw/feature/hills.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/feature/hills.py -------------------------------------------------------------------------------- /alpharaw/feature/isotope_pattern.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/feature/isotope_pattern.py -------------------------------------------------------------------------------- /alpharaw/legacy_msdata/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/legacy_msdata/mgf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/legacy_msdata/mgf.py -------------------------------------------------------------------------------- /alpharaw/match/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/match/mass_calibration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/match/mass_calibration.py -------------------------------------------------------------------------------- /alpharaw/match/match_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/match/match_utils.py -------------------------------------------------------------------------------- /alpharaw/match/psm_match.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/match/psm_match.py -------------------------------------------------------------------------------- /alpharaw/match/psm_match_alphatims.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/match/psm_match_alphatims.py -------------------------------------------------------------------------------- /alpharaw/match/spec_finder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/match/spec_finder.py -------------------------------------------------------------------------------- /alpharaw/ms_data_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/ms_data_base.py -------------------------------------------------------------------------------- /alpharaw/mzml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/mzml.py -------------------------------------------------------------------------------- /alpharaw/mzml_io/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/mzml_io/cv_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/mzml_io/cv_constants.py -------------------------------------------------------------------------------- /alpharaw/mzml_io/mzml_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/mzml_io/mzml_writer.py -------------------------------------------------------------------------------- /alpharaw/raw_access/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/raw_access/clr_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/raw_access/clr_utils.py -------------------------------------------------------------------------------- /alpharaw/raw_access/pysciexwifffilereader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/raw_access/pysciexwifffilereader.py -------------------------------------------------------------------------------- /alpharaw/raw_access/pythermorawfilereader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/raw_access/pythermorawfilereader.py -------------------------------------------------------------------------------- /alpharaw/resources/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/resources/README.md -------------------------------------------------------------------------------- /alpharaw/resources/psi-ms.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/resources/psi-ms.owl -------------------------------------------------------------------------------- /alpharaw/sciex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/sciex.py -------------------------------------------------------------------------------- /alpharaw/thermo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/thermo.py -------------------------------------------------------------------------------- /alpharaw/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/utils/centroiding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/utils/centroiding.py -------------------------------------------------------------------------------- /alpharaw/utils/df_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/utils/df_processing.py -------------------------------------------------------------------------------- /alpharaw/utils/ms_path_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/utils/ms_path_utils.py -------------------------------------------------------------------------------- /alpharaw/utils/timstof.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/utils/timstof.py -------------------------------------------------------------------------------- /alpharaw/viz/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/viz/df_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/viz/df_utils.py -------------------------------------------------------------------------------- /alpharaw/viz/plot_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/viz/plot_utils.py -------------------------------------------------------------------------------- /alpharaw/viz/psm_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/viz/psm_plot.py -------------------------------------------------------------------------------- /alpharaw/viz/xic_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/viz/xic_plot.py -------------------------------------------------------------------------------- /alpharaw/viz/xic_plot_tims.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/viz/xic_plot_tims.py -------------------------------------------------------------------------------- /alpharaw/wrappers/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /alpharaw/wrappers/alphapept_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/wrappers/alphapept_wrapper.py -------------------------------------------------------------------------------- /alpharaw/wrappers/alphatims_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/alpharaw/wrappers/alphatims_wrapper.py -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/build_docs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/build_docs.sh -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/match/match_utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/match/match_utils.rst -------------------------------------------------------------------------------- /docs/match/psm_match.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/match/psm_match.rst -------------------------------------------------------------------------------- /docs/match/spec_finder.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/match/spec_finder.rst -------------------------------------------------------------------------------- /docs/match_modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/match_modules.rst -------------------------------------------------------------------------------- /docs/reader_modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/reader_modules.rst -------------------------------------------------------------------------------- /docs/readers/mgf.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/readers/mgf.rst -------------------------------------------------------------------------------- /docs/readers/ms_data_base.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/readers/ms_data_base.rst -------------------------------------------------------------------------------- /docs/readers/mzml.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/readers/mzml.rst -------------------------------------------------------------------------------- /docs/readers/sciex.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/readers/sciex.rst -------------------------------------------------------------------------------- /docs/readers/thermo.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/readers/thermo.rst -------------------------------------------------------------------------------- /docs/tutorials.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/tutorials.rst -------------------------------------------------------------------------------- /docs/tutorials/base_settings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/tutorials/base_settings.ipynb -------------------------------------------------------------------------------- /docs/tutorials/ms_methods.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/tutorials/ms_methods.ipynb -------------------------------------------------------------------------------- /docs/tutorials/raw_readers.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/tutorials/raw_readers.ipynb -------------------------------------------------------------------------------- /docs/tutorials/spectrum_peak_df_connection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/tutorials/spectrum_peak_df_connection.png -------------------------------------------------------------------------------- /docs/viz/df_utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/viz/df_utils.rst -------------------------------------------------------------------------------- /docs/viz/plot_utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/viz/plot_utils.rst -------------------------------------------------------------------------------- /docs/viz/psm_plot.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/viz/psm_plot.rst -------------------------------------------------------------------------------- /docs/viz/xic_plot.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/viz/xic_plot.rst -------------------------------------------------------------------------------- /docs/viz_modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/docs/viz_modules.rst -------------------------------------------------------------------------------- /misc/CLA.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/misc/CLA.md -------------------------------------------------------------------------------- /misc/pip_install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/misc/pip_install.sh -------------------------------------------------------------------------------- /nbs/alpharaw_to_alphapept.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs/alpharaw_to_alphapept.ipynb -------------------------------------------------------------------------------- /nbs/psm_match_alphatims.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs/psm_match_alphatims.ipynb -------------------------------------------------------------------------------- /nbs/test_dia_matching.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs/test_dia_matching.ipynb -------------------------------------------------------------------------------- /nbs/test_tims_match.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs/test_tims_match.ipynb -------------------------------------------------------------------------------- /nbs/test_viz.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs/test_viz.ipynb -------------------------------------------------------------------------------- /nbs_tests/feature_finding.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/feature_finding.ipynb -------------------------------------------------------------------------------- /nbs_tests/legacy_msdata/mgf.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/legacy_msdata/mgf.ipynb -------------------------------------------------------------------------------- /nbs_tests/legacy_msdata/mzml.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/legacy_msdata/mzml.ipynb -------------------------------------------------------------------------------- /nbs_tests/match/match_utils.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/match/match_utils.ipynb -------------------------------------------------------------------------------- /nbs_tests/match/psm_match.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/match/psm_match.ipynb -------------------------------------------------------------------------------- /nbs_tests/test_alphatims_wrapper.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/test_alphatims_wrapper.ipynb -------------------------------------------------------------------------------- /nbs_tests/test_data/small.pwiz.1.1.mzML: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/test_data/small.pwiz.1.1.mzML -------------------------------------------------------------------------------- /nbs_tests/test_viz_multinotch.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/test_viz_multinotch.ipynb -------------------------------------------------------------------------------- /nbs_tests/wrappers/alphatims_wrapper.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/nbs_tests/wrappers/alphatims_wrapper.ipynb -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/pyproject.toml -------------------------------------------------------------------------------- /release/common/build_wheel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/release/common/build_wheel.sh -------------------------------------------------------------------------------- /requirements/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/requirements/requirements.txt -------------------------------------------------------------------------------- /requirements/requirements_development.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/requirements/requirements_development.txt -------------------------------------------------------------------------------- /requirements/requirements_docs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/requirements/requirements_docs.txt -------------------------------------------------------------------------------- /requirements/requirements_loose.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/requirements/requirements_loose.txt -------------------------------------------------------------------------------- /requirements/requirements_tests.txt: -------------------------------------------------------------------------------- 1 | matplotlib 2 | seaborn 3 | pytest 4 | nbmake==1.5.3 5 | requests 6 | -------------------------------------------------------------------------------- /requirements/requirements_viz.txt: -------------------------------------------------------------------------------- 1 | plotly 2 | #xarray 3 | #multipledispatch 4 | -------------------------------------------------------------------------------- /ruff-lint-strict.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/ruff-lint-strict.toml -------------------------------------------------------------------------------- /tests/download_test_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/tests/download_test_data.py -------------------------------------------------------------------------------- /tests/run_tests.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/tests/run_tests.sh -------------------------------------------------------------------------------- /tests/unit/test_mzml_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/tests/unit/test_mzml_writer.py -------------------------------------------------------------------------------- /tests/unit/test_remove_unused_peaks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/tests/unit/test_remove_unused_peaks.py -------------------------------------------------------------------------------- /tests/unit/test_requirements.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MannLabs/alpharaw/HEAD/tests/unit/test_requirements.py --------------------------------------------------------------------------------