quantms-utils 0.0.1__tar.gz

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Files changed (29) hide show
  1. quantms_utils-0.0.1/LICENSE +21 -0
  2. quantms_utils-0.0.1/PKG-INFO +75 -0
  3. quantms_utils-0.0.1/README.md +45 -0
  4. quantms_utils-0.0.1/pyproject.toml +31 -0
  5. quantms_utils-0.0.1/quantms_utils.egg-info/PKG-INFO +75 -0
  6. quantms_utils-0.0.1/quantms_utils.egg-info/SOURCES.txt +28 -0
  7. quantms_utils-0.0.1/quantms_utils.egg-info/dependency_links.txt +1 -0
  8. quantms_utils-0.0.1/quantms_utils.egg-info/entry_points.txt +2 -0
  9. quantms_utils-0.0.1/quantms_utils.egg-info/requires.txt +8 -0
  10. quantms_utils-0.0.1/quantms_utils.egg-info/top_level.txt +1 -0
  11. quantms_utils-0.0.1/quantmsutils/__init__.py +0 -0
  12. quantms_utils-0.0.1/quantmsutils/diann/__init__.py +0 -0
  13. quantms_utils-0.0.1/quantmsutils/diann/diann2mztab.py +1628 -0
  14. quantms_utils-0.0.1/quantmsutils/diann/dianncfg.py +141 -0
  15. quantms_utils-0.0.1/quantmsutils/features/__init__.py +0 -0
  16. quantms_utils-0.0.1/quantmsutils/features/sage_feature.py +38 -0
  17. quantms_utils-0.0.1/quantmsutils/mzml/__init__.py +0 -0
  18. quantms_utils-0.0.1/quantmsutils/mzml/mzml_statistics.py +231 -0
  19. quantms_utils-0.0.1/quantmsutils/psm/__init__.py +0 -0
  20. quantms_utils-0.0.1/quantmsutils/psm/psm_conversion.py +174 -0
  21. quantms_utils-0.0.1/quantmsutils/quantmsutilsc.py +41 -0
  22. quantms_utils-0.0.1/quantmsutils/rescoring/__init__.py +0 -0
  23. quantms_utils-0.0.1/quantmsutils/rescoring/ms2rescore.py +326 -0
  24. quantms_utils-0.0.1/quantmsutils/sdrf/__init__.py +0 -0
  25. quantms_utils-0.0.1/quantmsutils/sdrf/check_samplesheet.py +134 -0
  26. quantms_utils-0.0.1/quantmsutils/sdrf/extract_sample.py +46 -0
  27. quantms_utils-0.0.1/setup.cfg +7 -0
  28. quantms_utils-0.0.1/setup.py +66 -0
  29. quantms_utils-0.0.1/tests/test_commands.py +126 -0
quantms_utils-0.0.1/LICENSE ADDED
@@ -0,0 +1,21 @@
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+ MIT License
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+
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+ Copyright (c) 2024 BigBio Stack
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
quantms_utils-0.0.1/PKG-INFO ADDED
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+ Metadata-Version: 2.1
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+ Name: quantms-utils
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+ Version: 0.0.1
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+ Summary: Python package with scripts and helpers for the QuantMS workflow
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+ Home-page: https://www.github.com/bigbio/pyquantms
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+ Author: Yasset Perez-Riverol, Dai Chengxin
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+ Author-email: ypriverol@gmail.com
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+ License: MIT License
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+ Project-URL: Documentation, https://docs.quantms.org/en/latest/
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+ Project-URL: quantms Workflow, https://github.com/bigbio/quantms
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+ Project-URL: Tracker, https://github.com/bigbio/pyquantms/issues
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+ Keywords: quantms,Proteomics
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: Apache Software License
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+ Classifier: Operating System :: POSIX :: Linux
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+ Classifier: Programming Language :: Python :: 3 :: Only
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Requires-Python: >=3.8,<4
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: click
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+ Requires-Dist: sdrf-pipelines
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+ Requires-Dist: pyopenms
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+ Requires-Dist: ms2rescore==3.0.2
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+ Requires-Dist: psm-utils==0.8.0
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+ Requires-Dist: pydantic
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+ Requires-Dist: pandas
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+ Requires-Dist: numpy
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+
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+ # quantms-utils
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+ [![Python application](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml)
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+ [![Python package](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml)
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+ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/quantms-utils/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
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+ [![PyPI version](https://badge.fury.io/py/quantms-utils.svg)](https://badge.fury.io/py/quantms-utils)
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+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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+
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+ Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
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+
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+ The package is available on PyPI: [quantms-utils](https://pypi.org/project/quantms-utils/)
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+ ```
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+ pip install quantms-utils
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+ ```
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+
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+ ## Available Scripts
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+
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+ The following functionalities are available in the package:
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+
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+ ### Diann scripts
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+
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+ - `dianncfg` - Create a configuration file for Diann including enzymes, modifications, and other parameters.
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+ - `diann2mztab` - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab.
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+ The output formats are used for quality control and downstream analysis in quantms.
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+
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+ ### SDRF scripts
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+
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+ - `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/quantms-utils/blob/dev/tests/test_data/BSA_design_urls.tsv).
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+ - `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file.
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+
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+ ### ms2rescore scripts
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+
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+ - `ms2rescore` - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.
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+
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+ ### Features to percolator scripts
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+
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+ - `sage2feature` - The add_sage_feature function enhances an idXML file by appending additional features from a Sage feature table, excluding those generated by 'psm_file'.
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+
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+ ### Other scripts
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+
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+ - `psmconvert` - The convert_psm function converts peptide spectrum matches (PSMs) from an idXML file to a CSV file, optionally filtering out decoy matches. It extracts and processes data from both the idXML and an associated spectra file, handling multiple search engines and scoring systems.
71
+ - `mzmlstats` - The `mzmlstats` processes mass spectrometry data files in either `.mzML` or `Bruker .d` formats to extract and compile statistics about the spectra. It supports generating detailed or ID-only CSV files based on the spectra data.
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+
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+ ## Contributions and issues
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+
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+ Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/quantms-utils).
quantms_utils-0.0.1/README.md ADDED
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+ # quantms-utils
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+ [![Python application](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml)
3
+ [![Python package](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml)
4
+ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/quantms-utils/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
5
+ [![PyPI version](https://badge.fury.io/py/quantms-utils.svg)](https://badge.fury.io/py/quantms-utils)
6
+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
7
+
8
+ Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
9
+
10
+ The package is available on PyPI: [quantms-utils](https://pypi.org/project/quantms-utils/)
11
+ ```
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+ pip install quantms-utils
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+ ```
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+
15
+ ## Available Scripts
16
+
17
+ The following functionalities are available in the package:
18
+
19
+ ### Diann scripts
20
+
21
+ - `dianncfg` - Create a configuration file for Diann including enzymes, modifications, and other parameters.
22
+ - `diann2mztab` - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab.
23
+ The output formats are used for quality control and downstream analysis in quantms.
24
+
25
+ ### SDRF scripts
26
+
27
+ - `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/quantms-utils/blob/dev/tests/test_data/BSA_design_urls.tsv).
28
+ - `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file.
29
+
30
+ ### ms2rescore scripts
31
+
32
+ - `ms2rescore` - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.
33
+
34
+ ### Features to percolator scripts
35
+
36
+ - `sage2feature` - The add_sage_feature function enhances an idXML file by appending additional features from a Sage feature table, excluding those generated by 'psm_file'.
37
+
38
+ ### Other scripts
39
+
40
+ - `psmconvert` - The convert_psm function converts peptide spectrum matches (PSMs) from an idXML file to a CSV file, optionally filtering out decoy matches. It extracts and processes data from both the idXML and an associated spectra file, handling multiple search engines and scoring systems.
41
+ - `mzmlstats` - The `mzmlstats` processes mass spectrometry data files in either `.mzML` or `Bruker .d` formats to extract and compile statistics about the spectra. It supports generating detailed or ID-only CSV files based on the spectra data.
42
+
43
+ ## Contributions and issues
44
+
45
+ Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/quantms-utils).
quantms_utils-0.0.1/pyproject.toml ADDED
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+ [tool.poetry]
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+ name = "quantms-utils"
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+ version = "0.0.1"
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+ description = "Python scripts and helpers for the quantMS workflow"
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+ authors = ["Yasset Perez-Riverol", "Dai Chengxin"]
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+
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+ [build-system]
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+ requires = ["setuptools"]
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+ build-backend = "setuptools.build_meta"
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+
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+ [tool.poetry.dependencies]
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+ click = ">=7.0"
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+ pydantic = ">=1.10,<2"
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+ python = "^3.7"
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+ sdrf-pipelines = ">=0.0.26"
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+ pyopenms = ">=2.6.0"
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+ ms2rescore = ">=3.0.2"
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+ psm-utils = "==0.8.0"
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+ pandas = ">=1.0.0"
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+
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+ [tool.poetry.dev-dependencies]
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+ pytest = "*"
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+
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+ [tool.pytest.ini_options]
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+ minversion = "6.0"
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+ addopts = "-ra -q"
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+ testpaths = ["tests", ]
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+
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+ [tool.black]
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+ line-length = 88
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+ target-version = ['py37', 'py38', 'py39', 'py310', 'py311']
quantms_utils-0.0.1/quantms_utils.egg-info/PKG-INFO ADDED
@@ -0,0 +1,75 @@
1
+ Metadata-Version: 2.1
2
+ Name: quantms-utils
3
+ Version: 0.0.1
4
+ Summary: Python package with scripts and helpers for the QuantMS workflow
5
+ Home-page: https://www.github.com/bigbio/pyquantms
6
+ Author: Yasset Perez-Riverol, Dai Chengxin
7
+ Author-email: ypriverol@gmail.com
8
+ License: MIT License
9
+ Project-URL: Documentation, https://docs.quantms.org/en/latest/
10
+ Project-URL: quantms Workflow, https://github.com/bigbio/quantms
11
+ Project-URL: Tracker, https://github.com/bigbio/pyquantms/issues
12
+ Keywords: quantms,Proteomics
13
+ Classifier: Intended Audience :: Science/Research
14
+ Classifier: License :: OSI Approved :: Apache Software License
15
+ Classifier: Operating System :: POSIX :: Linux
16
+ Classifier: Programming Language :: Python :: 3 :: Only
17
+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
18
+ Classifier: Development Status :: 5 - Production/Stable
19
+ Requires-Python: >=3.8,<4
20
+ Description-Content-Type: text/markdown
21
+ License-File: LICENSE
22
+ Requires-Dist: click
23
+ Requires-Dist: sdrf-pipelines
24
+ Requires-Dist: pyopenms
25
+ Requires-Dist: ms2rescore==3.0.2
26
+ Requires-Dist: psm-utils==0.8.0
27
+ Requires-Dist: pydantic
28
+ Requires-Dist: pandas
29
+ Requires-Dist: numpy
30
+
31
+ # quantms-utils
32
+ [![Python application](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-app.yml)
33
+ [![Python package](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/quantms-utils/actions/workflows/python-package.yml)
34
+ [![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/quantms-utils/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
35
+ [![PyPI version](https://badge.fury.io/py/quantms-utils.svg)](https://badge.fury.io/py/quantms-utils)
36
+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
37
+
38
+ Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
39
+
40
+ The package is available on PyPI: [quantms-utils](https://pypi.org/project/quantms-utils/)
41
+ ```
42
+ pip install quantms-utils
43
+ ```
44
+
45
+ ## Available Scripts
46
+
47
+ The following functionalities are available in the package:
48
+
49
+ ### Diann scripts
50
+
51
+ - `dianncfg` - Create a configuration file for Diann including enzymes, modifications, and other parameters.
52
+ - `diann2mztab` - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab.
53
+ The output formats are used for quality control and downstream analysis in quantms.
54
+
55
+ ### SDRF scripts
56
+
57
+ - `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/quantms-utils/blob/dev/tests/test_data/BSA_design_urls.tsv).
58
+ - `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file.
59
+
60
+ ### ms2rescore scripts
61
+
62
+ - `ms2rescore` - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.
63
+
64
+ ### Features to percolator scripts
65
+
66
+ - `sage2feature` - The add_sage_feature function enhances an idXML file by appending additional features from a Sage feature table, excluding those generated by 'psm_file'.
67
+
68
+ ### Other scripts
69
+
70
+ - `psmconvert` - The convert_psm function converts peptide spectrum matches (PSMs) from an idXML file to a CSV file, optionally filtering out decoy matches. It extracts and processes data from both the idXML and an associated spectra file, handling multiple search engines and scoring systems.
71
+ - `mzmlstats` - The `mzmlstats` processes mass spectrometry data files in either `.mzML` or `Bruker .d` formats to extract and compile statistics about the spectra. It supports generating detailed or ID-only CSV files based on the spectra data.
72
+
73
+ ## Contributions and issues
74
+
75
+ Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/quantms-utils).
quantms_utils-0.0.1/quantms_utils.egg-info/SOURCES.txt ADDED
@@ -0,0 +1,28 @@
1
+ LICENSE
2
+ README.md
3
+ pyproject.toml
4
+ setup.cfg
5
+ setup.py
6
+ quantms_utils.egg-info/PKG-INFO
7
+ quantms_utils.egg-info/SOURCES.txt
8
+ quantms_utils.egg-info/dependency_links.txt
9
+ quantms_utils.egg-info/entry_points.txt
10
+ quantms_utils.egg-info/requires.txt
11
+ quantms_utils.egg-info/top_level.txt
12
+ quantmsutils/__init__.py
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+ quantmsutils/quantmsutilsc.py
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+ quantmsutils/diann/__init__.py
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+ quantmsutils/diann/diann2mztab.py
16
+ quantmsutils/diann/dianncfg.py
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+ quantmsutils/features/__init__.py
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+ quantmsutils/features/sage_feature.py
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+ quantmsutils/mzml/__init__.py
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+ quantmsutils/mzml/mzml_statistics.py
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+ quantmsutils/psm/__init__.py
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+ quantmsutils/psm/psm_conversion.py
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+ quantmsutils/rescoring/__init__.py
24
+ quantmsutils/rescoring/ms2rescore.py
25
+ quantmsutils/sdrf/__init__.py
26
+ quantmsutils/sdrf/check_samplesheet.py
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+ quantmsutils/sdrf/extract_sample.py
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+ tests/test_commands.py
quantms_utils-0.0.1/quantms_utils.egg-info/entry_points.txt ADDED
@@ -0,0 +1,2 @@
1
+ [console_scripts]
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+ quantmsutilsc = quantmsutils.quantmsutilsc:main
quantms_utils-0.0.1/quantms_utils.egg-info/requires.txt ADDED
@@ -0,0 +1,8 @@
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+ click
2
+ sdrf-pipelines
3
+ pyopenms
4
+ ms2rescore==3.0.2
5
+ psm-utils==0.8.0
6
+ pydantic
7
+ pandas
8
+ numpy
quantms_utils-0.0.1/quantms_utils.egg-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ quantmsutils
quantms_utils-0.0.1/quantmsutils/__init__.py ADDED
File without changes
quantms_utils-0.0.1/quantmsutils/diann/__init__.py ADDED
File without changes