Metadata-Version: 1.1
Name: py-ard
Version: 0.6.2
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)
        
            #
            # Reduce Allele
            #
            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'
        
            #
            # Reduce GL String
            #
            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('B14', 'lg')
            # >>> 'B*14:01g/B*14:02g/B*14:03g/B*14:04g/B*14:05g/B*14:06g/B*14:08g/B*14:09g/B*14:10g/B*14:11g/B*14:12g/B*14:13g/B*14:14g/B*14:15g/B*14:16g/B*14:17g/B*14:18g/B*14:19g/B*14:20g/B*14:21g/B*14:22g/B*14:23g/B*14:24g/B*14:25g/B*14:26g/B*14:27g/B*14:28g/B*14:29g/B*14:30g/B*14:31g/B*14:32g/B*14:33g/B*14:34g/B*14:35g/B*14:36g/B*14:37g/B*14:38g/B*14:39g/B*14:40g/B*14:42g/B*14:43g/B*14:44g/B*14:45g/B*14:46g/B*14:47g/B*14:48g/B*14:49g/B*14:50g/B*14:51g/B*14:52g/B*14:53g/B*14:54g/B*14:55g/B*14:56g/B*14:57g/B*14:58g/B*14:59g/B*14:60g/B*14:62g/B*14:63g/B*14:65g/B*14:66g/B*14:68g/B*14:70Qg/B*14:71g/B*14:73g/B*14:74g/B*14:75g/B*14:77g/B*14:82g/B*14:83g/B*14:86g/B*14:87g/B*14:88g/B*14:90g/B*14:93g/B*14:94g/B*14:95g/B*14:96g/B*14:97g/B*14:99g/B*14:102g'
        
        
        
        Command Line Tools
        ------------------
        
        .. code-block:: bash
        
            # Import the latest IMGT database
            $ pyard-import
            Created Latest py-ard database
        
            # Import particular version of IMGT database
            $ pyard-import --import-db-version 3.29.0
            Created py-ard version 3290 database
        
            # Import particular version of IMGT database and
            # replace the v2 to v3 mapping table
            $ pyard-import --import-db-version 3.29.0 --v2-to-v3-mapping map2to3.csv
            Created py-ard version 3290 database
            Updated v2_mapping table with 'map2to3.csv' mapping file.
        
            # Replace the Latest IMGT database with V2 mappings
            $ pyard-import  --v2-to-v3-mapping map2to3.csv
        
            # Reduce a gl string from command line
            $ pyard --gl 'A*01:AB' -r lgx
            A*01:01/A*01:02
        
            $ pyard --gl 'DRB1*08:XX' -r G
            DRB1*08:01:01G/DRB1*08:02:01G/DRB1*08:03:02G/DRB1*08:04:01G/DRB1*08:05/ ...
        
            $ pyard -v 3290 --gl 'A1' -r lgx
            A*01:01/A*01:02/A*01:03/A*01:06/A*01:07/A*01:08/A*01:09/A*01:10/A*01:12/ ...
        
        
        =======
        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
Classifier: Programming Language :: Python :: 3.9
Provides: pyard
