pymzid 0.3.2

pymzid reads in mzidentml files from proteomics search engine

Pymzid

Reads in mzid files from protein identification results in mass spectrometry/proteomics experiments

Installation and Usage

Install Python 3.7+ and pip. See instructions on Python website for specific instructions for your operating system.

Pymzid can be installed from PyPI via pip. We recommend using a virtual environment.

$ pip install pymzid

Launch as a standalone:

$ python -m pymzid path/to/mzid -o path/to/out

Alternatively:

$ pymzid

Use as a module:

from pymzid.read_mzid import Mzid

mzid = Mzid("path/to/mzid")
mzid.read_psm()

gives a pandas object under mzid.psm_df

To test that the installation can load test data files in tests/data:

$ pip install tox
$ tox

To run the test Percolator data and print the output to home:

$ python -m pymzid tests/data/comet_percolator/percolator.target.mzid -o ~  

Dependencies

Pymzid is tested in Python 3.7 and 3.8 and uses the following packages:

pandas==1.0.4
tqdm==4.46.1

Contributing

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

Authors

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

See also the list of contributors who participated in this project.

License

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