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 ~

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

pandas==1.0.4
tqdm==4.46.1

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

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

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