Metadata-Version: 2.1
Name: quantms-utils
Version: 0.0.15
Summary: Python scripts and helpers for the quantMS workflow
License: MIT
Keywords: quantms,proteomics,mass-spectrometry,data-analysis,big data
Author: Yasset Perez-Riverol
Author-email: ypriverol@gmail.com
Requires-Python: >=3.8,<3.11
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: click
Requires-Dist: deepLC (==2.2.38)
Requires-Dist: ms2rescore (==3.0.3)
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: protobuf (==3.19.6)
Requires-Dist: psm-utils (==0.8.3)
Requires-Dist: pyarrow
Requires-Dist: pygam
Requires-Dist: pyopenms
Requires-Dist: scipy (==1.13.1)
Requires-Dist: sdrf-pipelines (>=0.0.31)
Project-URL: GitHub, https://github.com/bigbio/quantms-utils
Project-URL: LICENSE, https://github.com/bigbio/quantms-utils/blob/main/LICENSE
Project-URL: PyPi, https://pypi.org/project/quantms-utils/
Project-URL: Quantms, https://quantms.org
Description-Content-Type: text/markdown

# quantms-utils
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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.

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'.
- `spectrum2feature`  - Add the signal-to-noise ratio (SNR) to the feature table for percolator.

### 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).

