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ARD reduction for HLA with Python

Project description

py-ard

PyPi Version

ARD reduction for HLA with Python

py-ard works with Python 3.8 and higher.

Install from PyPi

pip install py-ard

Install from source

python3 -m venv venv
source venv/bin/activate

python setup.py install

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

# Run unit-tests
python -m unittest tests.test_pyard

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

The cache size of pre-computed reductions can be changed from the default of 1000 (not working: will be fixed in a later release.)

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 different directory for the cached data.

ard = pyard.ARD('3290', data_dir='/tmp/py-ard')

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 IMGT HLA database

ard = pyard.ARD()

Reduce Typings

Reduce a single locus HLA Typing.

allele = "A*01:01:01"

ard.redux_gl(allele, 'G')
# >>> 'A*01:01:01G'

ard.redux_gl(allele, 'lg')
# >>> 'A*01:01g'

ard.redux_gl(allele, 'lgx')
# >>> 'A*01:01'

Reduce an ambiguous GL String

# 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'

You 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'

Valid Reduction Types

Reduction Type Description
G Reduce to G Group Level
lg Reduce to 2 field ARD level (append g)
lgx Reduce to 2 field ARD level
W Reduce/Expand to 3 field WHO nomenclature level
exon Reduce/Expand to exon level
U2 Reduce to 2 field unambiguous level

Command Line Tools

Using py-ard from the command line

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 from a CSV file.

$ 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.

Reinstall a particular IMGT database

pyard-import --db-version 3340 --re-install

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

Show the status of all py-ard databases

$ pyard-status

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 # For a particular version of DB
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/ ...

Batch Reduce a CSV file

pyard-csv-reduce can be used to batch process a CSV file with HLA typings. See documentation for instructions on how to configure and run.

py-ard REST Service

Run py-ard as a service so that it can be accessed as a REST service endpoint.

Build the docker image:

make docker-build

Build the docker and run it with:

make docker

The endpoint should then be available at localhost:8080

======= History

0.0.1 (2018-02-12)

  • First release on PyPI.

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