Metadata-Version: 2.1
Name: pytmt
Version: 0.4.1
Summary: pytmt returns ms2 tmt quantification values from Crux Percolator output
Home-page: https://github.com/ed-lau/pytmt
Author: Edward Lau
Author-email: edward.lau@cuanschutz.edu
License: UNKNOWN
Project-URL: Source, https://github.com/ed-lau/pytmt
Project-URL: Lau Lab Colorado, https://laulab.net
Keywords: scientific proteomics mass-spectrometry
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6, <4
Description-Content-Type: text/markdown
License-File: LICENSE.md

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

## Getting Started


#### Requirements

Install Python 3.7+ 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/psms.txt -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/percolator.target.psms.txt -o ~/Desktop/pytmt2
    

### Prerequisites

pytmt is tested in Python 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](https://github.com/ed-lau)
* **Maggie Lam, PhD** - *Code/design* - [Maggie-Lam](https://github.com/Maggie-Lam)


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


