Metadata-Version: 1.1
Name: py-ard
Version: 0.4.0
Summary: ARD reduction for HLA with python
Home-page: https://github.com/nmdp-bioinformatics/py-ard
Author: CIBMTR
Author-email: cibmtr-pypi@nmdp.org
License: LGPL 3.0
Description: ===============================
        py-ard
        ===============================
        
        
        .. image:: https://img.shields.io/pypi/v/py-ard.svg
                :target: https://pypi.python.org/pypi/py-ard
        
        .. image:: https://readthedocs.org/projects/pyars/badge/?version=latest
                :target: https://pyard.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        ARD reduction for HLA with python
        
        * Free software: LGPL 3.0
        * Documentation: https://pyard.readthedocs.io.
        
        
        Install from source
        -------------------
        
        .. code-block::
        
            python3 -m venv venv
            source venv/bin/activate
        
            python setup.py install
        
        Install from PyPi
        -----------------
        
        .. code-block::
        
            pip install py-ard
        
        Testing
        -------
        
        To run behavior-driven development (BDD) tests locally via the behave framework,
        you'll need to set up a virtual environment. See Install from source
        
        .. code-block::
        
            # Install test dependencies
            pip install --upgrade pip
            pip install -r test-requirements.txt
        
            # Running Behave and all BDD tests
            behave
        
        Example
        -------
        
        .. code-block:: python3
        
            import pyard
        
            # Initialize ARD object with a version of IMGT HLA database
            ard = pyard.ARD(3290)
        
            # You can specify a data directory for temp files
            # ard = pyard.ARD('3290', data_dir='/tmp/py-ard')
        
            # Initialize with latest IMGT HLA database
            ard = pyard.ARD()
        
            # You can choose to refresh the MAC code for previously used versions
            # ard =  pyard.ARD(3290, refresh_mac=True)
        
            # Allele to reduce
            allele = "A*01:01:01"
        
            ard.redux(allele, 'G')
            # 'A*01:01:01G'
        
            ard.redux(allele, 'lg')
            # 'A*01:01g'
        
            ard.redux(allele, 'lgx')
            # 'A*01:01'
        
            ard.redux_gl("A*01:01/A*01:01N+A*02:AB^B*07:02+B*07:AB", "G")
            # 'B*07:02:01G+B*07:02:01G^A*01:01:01G+A*02:01:01G/A*02:02'
        
            # py-ard can also reduce serology based typings
            ard.redux_gl('HLA-A*10^HLA-A*9', 'lg')
            # 'HLA-A*24:19g/HLA-A*24:22g^HLA-A*26:01g/HLA-A*26:10g/HLA-A*26:15g/HLA-A*26:92g/HLA-A*66:01g/HLA-A*66:03g'
        
        
        
        
        =======
        History
        =======
        
        0.0.1 (2018-02-12)
        ------------------
        
        * First release on PyPI.
        
Keywords: pyard
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
