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ARD reduction for HLA with Python

Project description

py-ard

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ARD reduction for HLA with Python

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)

#
# 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('HLA-A*10^HLA-A*9', 'lg')
# >>> ard_gl
# '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'

Command Line Tools

# 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.

Project details


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