# 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.
### 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).
Raw data
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