py-ard 0.6.0

从源安装

python3 -m venv venv
source venv/bin/activate

python setup.py install

从PyPi安装

测试

通过behave框架在本地运行行为驱动开发（BDD）测试， 您需要设置一个虚拟环境。请参见从源安装

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

# Running Behave and all BDD tests
behave

示例

importpyard# Initialize ARD object with a version of IMGT HLA databaseard=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 databaseard=pyard.ARD()# You can choose to refresh the MAC code for previously used versions# ard =  pyard.ARD(3290, refresh_mac=True)# Allele to reduceallele="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 typingsard.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'

命令行工具

# 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.

# 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/ ...