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@@ -15,5 +15,5 @@ full_name: Mario Picciani | |
| email: [email protected] | ||
| project_name: spectrum_io | ||
| project_short_description: IO related functionalities for oktoberfest. | ||
| version: 0.5.0 | ||
| version: 0.6.0 | ||
| license: MIT | ||
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| # Spectrum IO | ||
| [](https://pypi.org/project/spectrum_io/) | ||
| [](https://pypi.org/project/spectrum_io) | ||
| [](https://opensource.org/licenses/MIT) | ||
| [](https://spectrum-io.readthedocs.io/) | ||
| [](https://github.com/wilhelm-lab/spectrum_io/actions?workflow=Package) | ||
| [](https://github.com/wilhelm-lab/spectrum_io/actions?workflow=Tests) | ||
| [](https://codecov.io/gh/wilhelm-lab/spectrum_io) | ||
| [](https://github.com/pre-commit/pre-commit) | ||
| [](https://github.com/psf/black) | ||
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| Spectrum IO is a package primarily developed for usage within oktoberfest (https://github.com/wilhelm-lab/oktoberfest). It handles file conversions and input / output operations for oktoberfest. | ||
| # Spectrum IO: File / Data Conversion for Mass Spec data within the Oktoberfest ecosystem | ||
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| ## Installation | ||
| spectrum_io is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest). | ||
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| ### Prerequisites | ||
| It provides the following functionalities: | ||
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| If you want to convert raw files to mzml, make sure you have ThermoRawFileParser (https://github.com/compomics/ThermoRawFileParser) installed. | ||
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| If you are on linux or MacOS, make sure mono (https://www.mono-project.com/) is installed (for ThermoRawFileParser). | ||
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| ### Using pip | ||
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| ```bash | ||
| pip install oktoberfest | ||
| ``` | ||
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| ## Features | ||
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| - Read search results from different search engines (Mascot, MaxQuant, MSFragger, MS Amanda) and transform them to the internal format used by oktoberfest | ||
| - Read thermo raw files and convert them to mzml, required by oktoberfest | ||
| - Read a fasta file and digest with various configurations (protease, missed cleavages, length of peptides, fragmentation, ...) for spectral library generation | ||
| - Create spectral libraries from peptide lists and output as dlib, msp or spectronaut(csv) format | ||
| - read and write data created as part of oktoberfest in hdf5 libraries | ||
| - read search results from different search engines (MaxQuant, MSFragger, Sage, Xisearch) or a generic csv format and transform them to the internal format for rescoring with oktoberfest | ||
| - extraction of MS2 level spectra from .RAW files and conversion to to mzML for rescoring with oktoberfest | ||
| - spectra extraction from .d folders, conversion to .hdf5 format, and aggregation to MS2 level with metadata from a MaxQuant search for timsTOF rescoring with oktoberfest | ||
| - in-silico digestion of a fasta file with various configuration options (protease, missed cleavages, length of peptides, fragmentation, ...) for spectral library generation with oktoberfest | ||
| - write spectral libraries in dlib, msp, or spectronaut(csv) format | ||
| - parquet file creation for peptide prediction model development and refinement within DLOmix | ||
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| ## Documentation | ||
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| Please refer to https://spectrum-io.readthedocs.io for further documentation. | ||
| The official documentation can be found at https://spectrum-fundamentals.readthedocs.io | ||
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| ## How to cite | ||
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| ## License | ||
| Please always cite the main publication: | ||
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| The project is licensed under the [MIT license](https://github.com/wilhelm-lab/spectrum_io/blob/main/LICENSE). | ||
| [Oktoberfest] Picciani M, Gabriel W, Giurcoiu VG et al. (2023), _Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit_, [Proteomics](https://doi.org/10.1002/pmic.202300112) |
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| .. module:: spectrum_io | ||
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| .. automodule:: spectrum_io | ||
| :noindex: | ||
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| API | ||
| === | ||
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| Import SpectrumIO using | ||
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| .. code-block:: python | ||
| import spectrum_io as specio | ||
| File conversions | ||
| ---------------- | ||
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| .. module:: spectrum_io.d | ||
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| .. currentmodule:: spectrum_io | ||
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| Todo: add functions for bruker d conversions here | ||
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| .. autosummary:: | ||
| :toctree: api/d | ||
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| .. module:: spectrum_io.raw | ||
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| .. currentmodule:: spectrum_io | ||
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| Todo: add functions for thermoraw here | ||
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| Modstring conversions | ||
| --------------------- | ||
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| Todo | ||
| ---- | ||
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| other modules | ||
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| .. sidebar:: Key Contributors | ||
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| Current developers | ||
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| * `Mario Picciani <https://github.com/picciama>`_: lead developer since 2022, maintainer | ||
| * `Mostafa Kalhor <https://github.com/mostafakalhor>`_: developer, crosslinking | ||
| * `Wassim Gabriel <https://github.com/WassimG>`_: developer, PTMs, neutral losses, GUI | ||
| * `Arne van den Berg <https://github.com/arne-vdb>`_: developer, diverse contributions | ||
| * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_: developer, diverse contributions | ||
| * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_: developer, Koina, GUI | ||
| * `Armin Soleymaniniya <https://github.com/arminsl>`_: developer, GUI | ||
| * `Ayla Schröder <https://github.com/ayla-s>`_: developer, pickedGroupFDR | ||
| * Zixuan Xiao: developer, GUI | ||
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| Previous developers | ||
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| * `Matthew The <https://github.com/MatthewThe>`_: developer, percolator | ||
| * `Omar Shouman <https://github.com/omsh>`_: developer, diverse contributions | ||
| * Firas Hamood: developer, diverse contributions | ||
| * Cecilia Jensen: developer, diverse contributions | ||
| * Julian Mueller: developer, diverse contributions | ||
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| Other roles | ||
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| * `Mathias Wilhelm <https://github.com/mwilhelm42>`_: advisor and PI of wilhelmlab |
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| @import "basic.css"; | ||
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| /*Set max width to none so the theme uses all available width*/ | ||
| .wy-nav-content { | ||
| max-width: none; | ||
| max-width: 1200px; | ||
| } | ||
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| .wy-side-nav-search { | ||
| background-color: inherit; | ||
| } | ||
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| table.align-default { | ||
| text-align: left; | ||
| } | ||
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| .fixed-table th:first-child, | ||
| .fixed-table td:first-child, | ||
| .autosummary th:first-child, | ||
| .autosummary td:first-child { | ||
| min-width: 250px; | ||
| } | ||
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| .autosummary th:first-child, | ||
| .autosummary td:first-child { | ||
| min-width: 400px; | ||
| } | ||
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| .fixed-table th:last-child, | ||
| .fixed-table td:last-child, | ||
| .autosummary th:last-child, | ||
| .autosummary td:last-child { | ||
| width: 100%; | ||
| } | ||
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| .fixed-table { | ||
| margin-left: 0; | ||
| } | ||
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| .wy-table-responsive table th p, | ||
| .wy-table-responsive table td p { | ||
| white-space: normal; | ||
| } | ||
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| .autosummary { | ||
| margin-left: 0 !important; | ||
| } | ||
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| .main-config-table tbody tr:nth-child(n + 4):nth-child(-n + 5) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .main-config-table tbody tr:nth-child(n + 7):nth-child(-n + 7) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .lib-rescore-config-table | ||
| tbody | ||
| tr:nth-child(n + 2):nth-child(-n + 5) | ||
| td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .lib-rescore-config-table tbody tr:nth-last-child(-n + 2) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .lib-config-table tbody tr:nth-child(n + 2):nth-child(-n + 3) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .lib-config-table tbody tr:nth-last-child(-n + 6) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .digest-config-table tbody tr:not(:first-child) td:nth-child(1) { | ||
| padding-left: 50px; | ||
| } | ||
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| .date { | ||
| font-size: 50%; | ||
| } |
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| :github_url: {{ fullname | modurl }} | ||
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| {% extends "!autosummary/base.rst" %} | ||
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| .. http://www.sphinx-doc.org/en/stable/ext/autosummary.html#customizing-templates |
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