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Command Line Tool py-ard-import to import a new database
Command Line Tool `py-ard` to reduce a GL String
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‎README.rst‎

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@@ -88,3 +88,31 @@ Example
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# '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'
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Command Line Tools
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------------------
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.. code-block:: bash
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# Import the latest IMGT database
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$ pyard-import
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Created Latest py-ard database
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# Import particular version of IMGT database
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$ pyard-import --import-db-version 3.29.0
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Created py-ard version 3290 database
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# Import particular version of IMGT database and
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# replace the v2 to v3 mapping table
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$ pyard-import --import-db-version 3.29.0 --v2-to-v3-mapping map2to3.csv
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Created py-ard version 3290 database
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Updated v2_mapping table with 'map2to3.csv' mapping file.
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# Reduce a gl string from command line
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$ pyard --gl 'A*01:AB' -r lgx
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A*01:01/A*01:02
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$ pyard --gl 'DRB1*08:XX' -r G
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DRB1*08:01:01G/DRB1*08:02:01G/DRB1*08:03:02G/DRB1*08:04:01G/DRB1*08:05/ ...
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$ pyard -v 3290 --gl 'A1' -r lgx
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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/ ...

‎scripts/pyard‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# py-ard
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# Copyright (c) 2020 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
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#
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# This library is free software; you can redistribute it and/or modify it
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# under the terms of the GNU Lesser General Public License as published
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# by the Free Software Foundation; either version 3 of the License, or (at
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# your option) any later version.
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#
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# This library is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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# License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public License
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# along with this library; if not, write to the Free Software Foundation,
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# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
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#
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# > http://www.fsf.org/licensing/licenses/lgpl.html
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# > http://www.opensource.org/licenses/lgpl-license.php
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#
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import argparse
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import pyard
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def get_imgt_version(imgt_version):
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if imgt_version:
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version = imgt_version.replace('.', '')
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if version.isdigit():
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return version
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raise RuntimeError(f"{imgt_version} is not a valid IMGT database version number")
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return None
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(
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usage="""[-v <IMGT DB Version>] [gl-string redux_type]""",
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description="""py-ard tool to redux GL String"""
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)
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parser.add_argument(
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"-v",
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"--imgt-version",
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dest="imgt_version"
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)
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parser.add_argument(
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"--gl",
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required=True,
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dest="gl_string"
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)
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parser.add_argument(
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"-r",
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choices=['G', 'lg', 'lgx'],
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required=True,
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dest="redux_type"
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)
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args = parser.parse_args()
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imgt_version = get_imgt_version(args.imgt_version)
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if imgt_version:
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ard = pyard.ARD(imgt_version)
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else:
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ard = pyard.ARD()
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print(ard.redux_gl(args.gl_string, args.redux_type))
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del ard

‎scripts/pyard-import‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# py-ard
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# Copyright (c) 2020 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
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#
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# This library is free software; you can redistribute it and/or modify it
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# under the terms of the GNU Lesser General Public License as published
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# by the Free Software Foundation; either version 3 of the License, or (at
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# your option) any later version.
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#
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# This library is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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# License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public License
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# along with this library; if not, write to the Free Software Foundation,
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# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
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#
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# > http://www.fsf.org/licensing/licenses/lgpl.html
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# > http://www.opensource.org/licenses/lgpl-license.php
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#
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import argparse
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import pathlib
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import pyard
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from pyard import db
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import pandas as pd
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def get_imgt_version(imgt_version):
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if imgt_version:
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version = imgt_version.replace('.', '')
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if version.isdigit():
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return version
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raise RuntimeError(f"{imgt_version} is not a valid IMGT database version number")
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return None
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def get_data_dir(data_dir):
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if data_dir:
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path = pathlib.Path(data_dir)
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if not path.exists() or not path.is_dir():
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raise RuntimeError(f"{data_dir} is not a valid directory")
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return data_dir
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def get_v2_v3_mapping(v2_v3_mapping):
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if v2_v3_mapping:
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path = pathlib.Path(v2_v3_mapping)
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if not path.exists() or not path.is_file():
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raise RuntimeError(f"{data_dir} is not a valid file")
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df = pd.read_csv(path, names=['v2', 'v3'])
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return df.set_index('v2')['v3'].to_dict()
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return None
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(
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usage="""[--import-db-version <IMGT DB Version>]\
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[--data-dir <directory for db file>]\
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[--v2-to-v3-mapping <V2 to V3 mapping CSV file>]""",
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description="""py-ard tool to generate reference SQLite database.\
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Allows updating db with custom mappings."""
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)
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parser.add_argument(
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"--import-db-version",
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dest="imgt_version"
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)
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parser.add_argument(
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"--data-dir",
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dest="data_dir"
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)
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parser.add_argument(
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"--v2-to-v3-mapping",
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dest="v2_v3_mapping"
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)
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args = parser.parse_args()
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imgt_version = get_imgt_version(args.imgt_version)
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# print(imgt_version)
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data_dir = get_data_dir(args.data_dir)
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# print(data_dir)
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v2_to_v3_dict = get_v2_v3_mapping(args.v2_v3_mapping)
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# print(len(v2_to_v3_dict))
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if imgt_version:
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ard = pyard.ARD(imgt_version=imgt_version, data_dir=data_dir)
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print(f"Created py-ard version {imgt_version} database")
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else:
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ard = pyard.ARD(data_dir=data_dir)
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print(f"Created Latest py-ard database")
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del ard
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if v2_to_v3_dict:
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db_connection = db.create_db_connection(data_dir, imgt_version, ro=False)
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db.save_dict(db_connection, table_name='v2_mapping',
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dictionary=v2_to_v3_dict, columns=('v2', 'v3'))
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print(f"Updated v2_mapping table with '{args.v2_v3_mapping}' mapping file.")

‎setup.py‎

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'pandas>=1.1.4'
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]
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test_requirements = [
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# TODO: put package test requirements here
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'behave==1.2.6',
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'PyHamcrest==2.0.2'
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]
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setup(
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name='py-ard',
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version='0.5.1',
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description="ARD reduction for HLA with python",
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description="ARD reduction for HLA with Python",
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long_description=readme + '\n\n' + history,
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author="CIBMTR",
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author_email='[email protected]',
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url='https://github.com/nmdp-bioinformatics/py-ard',
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packages=[
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'pyard',
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],
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package_dir={'pyard': 'pyard'},
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provides=['pyard'],
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scripts=[
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'scripts/pyard',
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'scripts/pyard-import',
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],
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install_requires=requirements,
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license="LGPL 3.0",
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zip_safe=False,

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