preprocessmzML 0.1.0

A package for preprocessing mzML files for ZooMS analysis

preprocessmzML

A simple python package for preprocessing mzML spectra using various filters and normalization techniques derived from the fantastic pyopenms package. This package supports baseline correction, smoothing, centroiding, and normalization of spectra from MALDI-TOF mass spectrometers.

Features

• Baseline Correction: Remove baseline using MorphologicalFilter
• Smoothing: Smooth the spectrum using Savitzky-Golay filter
• Centroiding: Pick peaks with PeakPickerHiRes
• Normalization: Normalize spectra with different methods (TIC, To the most intense peak)

Installation

Prerequisites

• Python 3.6 or higher
• pip (Python package installer)

macOS or Linux systems

1. Create and activate a virtual environment:

python3 -m venv preprocess_mzml
source venv/bin/activate

2. Install the package:

pip install preprocessmzML

Windows

1. Create and activate a virtual environment:

python -m venv venv
venv\Scripts\activate

2. Install the package:

pip install preprocessmzML

To install the package, use the following command:

pip install preprocessmzML

Usage

After installing the package, you can preprocess your mzML files from the command line (in a virtual environment as described above). I highly recommend running this workflow within a virtual environment to tackle version conflicts of modules used in this package.

Command-Line Interface (CLI)

preprocess_mzml --data_dir /path/to/mzML/files --output_base_dir /path/to/output/directory

Troubleshooting

If you encounter issues, please check the following:

• Ensure that the mzML files are correctly formatted and accessible.
• Verify that the output directory is writable.
• Check the parameter combinations for any invalid values.

Contributing

Contributions are always welcome. Feel free to submit a pull request or open an issue on Github.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Author

Bharath Nair [e-mail]; [e-mail]

Acknowledgements

• pyopenms
• pandas
• numpy
• matplotlib

This README.md includes:

• A brief introduction to the package and its features.
• Installation instructions.
• Usage examples.
• Detailed function documentation.
• Contribution guidelines.
• License information.
• Author information.
• Acknowledgements for dependencies.