pytmt 0.2.6

pytmt returns ms2 tmt quantification values from Crux Percolator output

PyTMT returns ms2 tandem mass tag quantification values from Crux/Percolator output.

Getting Started

Requirements

Install Python 3.6+ and pip. See instructions on Python website for specific instructions for your operating system.

Install pytmt from PyPI. We recommend using a virtual environment.

$ pip install pytmt

Running

Launch pytmt as a Python module (Usage/Help)

$ python -m pytmt

Console entry point:

$ pytmt

Example command:

$ python -m pytmt /path/to/mzml/ /path/to/percolator/ -o /path/to/output/

To test installation of test data files and download two test mzml files from ProteomeXchange:

$ pip install tox
$ tox

To run pytmt on the test data files and print the file to Desktop:

$ pytmt tests/data/mzml tests/data/percolator -o ~/Desktop/pytmt2

Prerequisites

pytmt is tested in Python 3.6, 3.7, and 3.8 and requires the following packages:

pandas>=1.0.4
pymzml==2.4.6
tqdm>=4.46.0

Contributing

Please contact us if you wish to contribute, and submit pull requests to us.

Authors

• Edward Lau, PhD - Code/design - ed-lau
• Maggie Lam, PhD - Code/design - Maggie-Lam

License

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