py-ard 0.4.0

ARD reduction for HLA with python

py-ard

ARD reduction for HLA with python

• Free software: LGPL 3.0

• Documentation: https://pyard.readthedocs.io.

Install from source

python3 -m venv venv
source venv/bin/activate

python setup.py install

Install from PyPi

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

# Install test dependencies
pip install --upgrade pip
pip install -r test-requirements.txt

# Running Behave and all BDD tests
behave

Example

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.