Using py‐ard in Python

Using py-ard from Python code

py-ard can be used in a program to reduce/expand HLA GL String representation. If pyard discovers an invalid Allele, it'll throw an Invalid Exception, not silently return an empty result.

Initialize py-ard

Import pyard package.

import pyard

Initialize ARD object with a version of IMGT HLA database

import pyard

ard = pyard.init('3510')

When processing a large numbers of typings, it's helpful to have a cache of previously calculated reductions to make similar typings reduce faster. The cache size of pre-computed reductions can be changed from the default of 1,000 by setting cache_size argument. This increases the memory footprint but will significantly increase the processing times for large number of reductions.

import pyard

max_cache_size = 1_000_000
ard = pyard.init('3510', cache_size=max_cache_size)

By default, the IPD-IMGT/HLA data is stored locally in $TMPDIR/pyard. This may be removed when your computer restarts. You can specify a different, more permanent directory for the cached data.

import pyard.ard

ard = pyard.init('3510', data_dir='/tmp/py-ard')

As MAC data changes frequently, you can choose to refresh the MAC code for current IMGT HLA database version.

ard.refresh_mac_codes()

The default initialization is to use the latest version of IPD-IMGT/HLA database.

import pyard

ard = pyard.init()

You can check the current version of IPD-IMGT/HLA database.

ard.get_db_version()

Reduce Typings

Note: Previous to version of 1.0.0 release of py-ard, there was redux and redux_gl methods on ard. They have been consolidated so that redux handles both GL Strings and individual alleles.

Reduce a single locus HLA Typing by specifying the allele/MAC/XX code and the reduction method to redux method.

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 an ambiguous GL String

# Reduce GL String
#
ard.redux("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'

You can also reduce serology based typings.

ard.redux('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'