quantms-utils 0.0.1__py3-none-any.whl

quantms_utils-0.0.1.dist-info/LICENSE

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+MIT License
+
+Copyright (c) 2024 BigBio Stack
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

quantms_utils-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: quantms-utils
+Version: 0.0.1
+Summary: Python package with scripts and helpers for the QuantMS workflow
+Home-page: https://www.github.com/bigbio/pyquantms
+Author: Yasset Perez-Riverol, Dai Chengxin
+Author-email: ypriverol@gmail.com
+License: MIT License
+Project-URL: Documentation, https://docs.quantms.org/en/latest/
+Project-URL: quantms Workflow, https://github.com/bigbio/quantms
+Project-URL: Tracker, https://github.com/bigbio/pyquantms/issues
+Keywords: quantms,Proteomics
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Development Status :: 5 - Production/Stable
+Requires-Python: >=3.8,<4
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: sdrf-pipelines
+Requires-Dist: pyopenms
+Requires-Dist: ms2rescore ==3.0.2
+Requires-Dist: psm-utils ==0.8.0
+Requires-Dist: pydantic
+Requires-Dist: pandas
+Requires-Dist: numpy
+
+# quantms-utils
+[![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)
+[![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)
+[![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)
+[![PyPI version](https://badge.fury.io/py/quantms-utils.svg)](https://badge.fury.io/py/quantms-utils)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
+
+The package is available on PyPI: [quantms-utils](https://pypi.org/project/quantms-utils/)
+```
+pip install quantms-utils
+```
+
+## Available Scripts 
+
+The following functionalities are available in the package:
+
+### Diann scripts
+
+- `dianncfg` - Create a configuration file for Diann including enzymes, modifications, and other parameters.
+- `diann2mztab` - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab.
+    The output formats are used for quality control and downstream analysis in quantms.
+
+### SDRF scripts
+
+- `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).
+- `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file. 
+
+### ms2rescore scripts
+
+- `ms2rescore` - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.
+
+### Features to percolator scripts
+
+- `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'.
+
+### Other scripts
+
+- `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.
+- `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.
+
+## Contributions and issues
+
+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.dist-info/RECORD

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+quantmsutils/diann/diann2mztab.py,sha256=uR1HN1MlD0rvEnSX9rJ6zsnvSKpOke5VPZdGLGNlGg4,59274
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+quantmsutils/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+quantmsutils/features/sage_feature.py,sha256=O4iCnYBmD7NtnNdsg_Dbm4M5qINOHyfT-ut5FPIv3Ys,1488
+quantmsutils/mzml/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+quantmsutils/mzml/mzml_statistics.py,sha256=AMI2VcMVt74ZlUqmr-OhZCL_3r4rNyD6b_yOwKh2Hm4,7780
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+quantmsutils/rescoring/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+quantmsutils/sdrf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+quantmsutils/sdrf/check_samplesheet.py,sha256=tpdrLYb5k_xaajCzHX4CtOFZRXVHykNYSR_rETAYq84,4400
+quantmsutils/sdrf/extract_sample.py,sha256=CVHntKSXkQOSWjuaYUiTyklRGkwZIVsUUekglVjGG50,1714
+quantms_utils-0.0.1.dist-info/LICENSE,sha256=1ROMIyV2fiUdem2FvA7a801c0EHmNLPBqxb6dRLcS3s,1069
+quantms_utils-0.0.1.dist-info/METADATA,sha256=7Ayz3W4-1Dk40QiQDo6dBwx5AabLnltiT9Q3_XzbkZQ,4217
+quantms_utils-0.0.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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+quantms_utils-0.0.1.dist-info/RECORD,,

quantms_utils-0.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

quantms_utils-0.0.1.dist-info/entry_points.txt

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+[console_scripts]
+quantmsutilsc = quantmsutils.quantmsutilsc:main

quantms_utils-0.0.1.dist-info/top_level.txt

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+quantmsutils