py-ard 0.6.9

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

# The cache size of pre-computed reductions can be changed
# from the default of 1000
pyard.max_cache_size = 1_000_000

# 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 current ARD db version
# ard.refresh_mac_codes()

# You can reinstall a particular IMGT database
# pyard-import --db-version 3340 --re-install
#
# 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

# Import the latest IMGT database
$ pyard-import
Created Latest py-ard database

# Import particular version of IMGT database
$ pyard-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 --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

# Refresh the MAC for the specified version
$ pyard-import --db-version 3450 --refresh-mac

# 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/ ...

# Show the status of all py-ard databases
$ pyard-status

History

0.0.1 (2018-02-12)

• First release on PyPI.