Metadata-Version: 2.1
Name: pymzid
Version: 0.3.1
Summary: pymzid reads in mzidentml files from proteomics search engine
Home-page: https://github.com/Lau-Lab/pymzid/
Author: Edward Lau
Author-email: edward.lau@cuanschutz.edu
License: UNKNOWN
Project-URL: Source, https://github.com/Lau-Lab/pymzid
Project-URL: Edward Lau Lab, https://www.laulab.net
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](https://github.com/ed-lau)
        
        See also the list of [contributors](https://github.com/Lau-Lab/pymzid/graphs/contributors) who participated in this project.
        
        
        ## License
        
        This project is licensed under the MIT License - see the [LICENSE.md](https://github.com/Lau-Lab/pymzid/blob/master/LICENSE.md) file for details
        
        
Keywords: scientific turnover kinetics proteomics mass-spectrometry
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
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 :: Only
Requires-Python: >=3.6, <4
Description-Content-Type: text/markdown
