pymzid reads in mzidentml files from proteomics search engine
Project description
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
Project details
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