py-ard 1.5.0

Description:

pyard 1.5.0

py-ard
Swiss army knife of HLA Nomenclature


Note:


Python Version 3.8 is no longer supported with the latest py-ard versions due to latest Pandas library not supporting 3.8. Please use py-ard==1.2.1 if using Python 3.8


ping mode is default. When in ping mode, alleles that do not have a G group, their corresponding P group is used.


Release 1.1.1 has extensive Serolgy related updates and affects Serology related data. Please rebuild the cache database if there's a missing Serology error.


pyard-import --re-install

Or set py-ard requirements to be py-ard<=1.1.1 for your dependency.

py-ard is ARD reduction for HLA in Python
Human leukocyte antigen (HLA) genes encode cell surface proteins that are important for immune regulation. Exons
encoding the Antigen Recognition Domain (ARD) are the most polymorphic region of HLA genes and are important for
donor/recipient HLA matching.
The history of allele typing methods has played a major role in determining resolution and ambiguity of reported HLA
values. Although
HLA nomenclature has not
always conformed to the same standard, it is now defined
by The WHO Nomenclature Committee for Factors of the HLA System. py-ard
is aware of the variation in historical resolutions and grouping and is able to translate from one representation to
another based on alleles published quarterly by IPD/IMGT-HLA.
Table of Contents

Installation

Install From PyPi
Install With Homebrew
Install From Source


Using py-ard

Using py-ard from Python
Using py-ard from R
Perform Reduxtion
DRBX blending
Expand/Lookup MAC


Command Line Tools

pyard-import Import Reference Data
pyard-status Show Statuses of Databases
pyard Redux
pyard-csv-reduce Batch Mode Redux


py-ard REST Webservice
Docker Deployment

Installation
py-ard works with Python 3.8 and higher.
Install from PyPi
pip install py-ard

Note: With py-ard version 1.0.0 and higher, the redux API has changed. If your use requires the older API, please
install with pip install py-ard==0.9.2
Install With Homebrew
On macOS, py-ard can be installed using Homebrew package manager.
This is very handy for using the command line versions of the tool without having to create virtual environments.
First time, you'd need to tap the nmdp-bioinformatics tap.
brew tap nmdp-bioinformatics/tap

Install py-ard
brew install py-ard

Homebrew will notify you as new versions of py-ard are released.
Install from source
Checkout the py-ard source code.
git clone https://github.com/nmdp-bioinformatics/py-ard.git
cd py-ard

Create and activate virtual environment. Install the py-ard dependencies.
make venv

source venv/bin/activate

make install

See Our Contribution Guide for open source contribution to py-ard.
Using py-ard
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 and initialize pyard package.
The default initialization is to use the latest version of IPD-IMGT/HLA database.
import pyard

ard = pyard.init()

Initialize py-ard with a particular version of IPD/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()

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'

Valid Reduction Types



Reduction Type
Description




G
Reduce to G Group Level


P
Reduce to P Group Level


lg
Reduce to 2 field ARD level (append g)


lgx
Reduce to 2 field ARD level


W
Reduce/Expand to full field(4,3,2) WHO nomenclature level


exon
Reduce/Expand to 3 field level


U2
Reduce to 2 field unambiguous level


S
Reduce to Serological level



Perform DRB1 blending with DRB3, DRB4 and DRB5
import pyard

pyard.dr_blender(drb1='HLA-DRB1*03:01+DRB1*04:01', drb3='DRB3*01:01', drb4='DRB4*01:03')
# >>> 'DRB3*01:01+DRB4*01:03'

MAC Codes
py-ard supports not only reducing to various types but helps in expanding and
looking up MAC representation. See MAC Service UI for detail.
Expand MAC
You can also use py-ard to expand MAC codes. Use expand_mac method on ard.
ard.expand_mac('HLA-A*01:BC')
# 'HLA-A*01:02/HLA-A*01:03'

Lookup MAC
Find the corresponding MAC code for an allele list GL String.
ard.lookup_mac('A*01:02/A*01:01/A*01:03')
# A*01:MN

CWD Reduction
Reduce a MAC code or an allele list GL String to CWD reduced list.
ard.cwd_redux("B*15:01:01/B*15:01:03/B*15:04/B*15:07/B*15:26N/B*15:27")
# => B*15:01/B*15:07

The above 2 methods can be chained to get back a MAC code that has a CWD reduced version.
ard.lookup_mac(ard.cwd_redux("B*15:01:01/B*15:01:03/B*15:04/B*15:07/B*15:26N/B*15:27"))
# 'B*15:AH'

Using py-ard from R code
py-ard works well from R as well. Please
see Using pyard from R language
page for detailed walkthrough.
Command Line Tools
Various command line interface (CLI) tools are available to use for managing local IPD-IMGT/HLA cache database, running
impromptu reduction queries and batch processing of CSV files.
For all tools, use --imgt-version and --data-dir to specify the IPD-IMGT/HLA database version and the directory
where the SQLite files are created.
pyard-import Import the latest IPD-IMGT/HLA database
pyard-import helps with importing and reinstalling of prepared IPD-IMGT/HLA and MAC data.
Use pyard-import -h to see all the options available.
$ pyard-import -h
usage: pyard-import [-h] [--list] [-i IMGT_VERSION] [-d DATA_DIR] [--v2-to-v3-mapping V2_V3_MAPPING] [--refresh-mac] [--re-install] [--skip-mac]

py-ard tool to generate reference SQLite database. Allows updating db with custom V2 to V3 mappings. Displays the list of available IMGT database
versions.

options:
-h, --help show this help message and exit
--list Show Versions of available IMGT Databases
-i IMGT_VERSION, --imgt-version IMGT_VERSION
Import supplied IMGT_VERSION DB Version
-d DATA_DIR, --data-dir DATA_DIR
Data directory to store imported data
--v2-to-v3-mapping V2_V3_MAPPING
V2 to V3 mapping CSV file
--refresh-mac Only refresh MAC data
--re-install reinstall a fresh version of database
--skip-mac Skip creating MAC mapping

Run pyard-import without any option to download and prepare the latest version of IPD-IMGT/HLA and MAC data.
$ 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 --imgt-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 --imgt-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 --imgt-version 3450 --refresh-mac

Skip MAC loading
You can skip loading MAC if you don't need by using --skip-mac
$ pyard-import --imgt-version 3150 --skip-mac

pyard-status Show database status
Show the statuses of all py-ard databases
pyard-status goes through all the available databases and checks all the tables that should be available. This is very
helpful to show all the databases, number of rows in each table, any missing tables and the stored IPD-IMGT/HLA version.
$ pyard-status

Use --data-dir to specify an alternate directory for cached database files.
$ pyard-status --data-dir ~/.pyard/
IMGT DB Version: Latest (3440)
There is a newer IMGT release than version 3440
Upgrade to latest version '3510' with 'pyard-import --re-install'
File: /Users/pbashyal/.pyard/pyard-Latest.sqlite3
Size: 533.37MB
-------------------------------------------
|Table Name |Rows |
|-----------------------------------------|
|dup_g | 59|
|dup_lgx | 1|
|g_group | 14223|
|p_group | 18872|
|lgx_group | 14223|
|exon_group | 12934|
|p_not_g | 1681|
|xx_codes | 1517|
|who_group | 30785|
|alleles | 32504|
|exp_alleles | 60|
|who_alleles | 30523|
|mac_codes | 1089379|
-------------------------------------------

pyard Redux quickly
pyard command can be used for quick reductions from the command line. Use --help option to see all the available
options.
$ pyard --help
usage: pyard [-h] [-v] [-d DATA_DIR] [-i IMGT_VERSION] [-g GL_STRING]
[-r {G,P,lg,lgx,W,exon,U2}] [--splits SPLITS]

py-ard tool to redux GL String

options:
-h, --help show this help message and exit
-v, --version IPD-IMGT/HLA DB Version number
-d DATA_DIR, --data-dir DATA_DIR
Data directory to store imported data
-i IMGT_VERSION, --imgt-version IMGT_VERSION
IPD-IMGT/HLA db to use for redux
-g GL_STRING, --gl GL_STRING
GL String to reduce
-r {G,P,lg,lgx,W,exon,U2}, --redux-type {G,P,lg,lgx,W,exon,U2}
Reduction Method
--splits SPLITS Find Broad and Splits

Reduce from command line by specifying any typing with -g or --gl option and the reduction method with -r
or --redux-type option.
$ pyard -g '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 -i 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/ ...

If the -r option is left out, pyard will print out the result of all reduction methods.
$ pyard -g 'A*01:01:01:01'
Reduction Method: G
-------------------
A*01:01:01G

Reduction Method: P
-------------------
A*01:01P

Reduction Method: lg
--------------------
A*01:01g

Reduction Method: lgx
---------------------
A*01:01

Reduction Method: W
-------------------
A*01:01:01:01

Reduction Method: exon
----------------------
A*01:01:01

Reduction Method: U2
--------------------
A*01:01

py-ard knows about the broad/splits of serology and DNA, you can find by using --splits option to pyard command.
$ pyard --splits "A*10"
A*10 = A*25/A*26/A*34/A*66

$ pyard --splits B14
B14 = B64/B65

pyard-csv-reduce Batch Reduce a CSV file
pyard-csv-reduce can be used to batch process a CSV file with HLA typings. See documentation for
detailed information about all the options.
py-ard REST Web Service
Run py-ard as a service so that it can be accessed as a REST service endpoint.
To start in debug mode, you can run the app.py script. The endpoint should then be available
at localhost:8080
$ python app.py
* Serving Flask app 'app'
* Debug mode: on
WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
* Running on all addresses (0.0.0.0)
* Running on http://127.0.0.1:8080
* Running on http://10.0.1.37:8080
Press CTRL+C to quit

Docker deployment of py-ard REST Web Service
For deploying to production, build a Docker image and use that image for deploying to a server.
Build the docker image:
make docker-build

builds a Docker image named pyard-service:latest
Build the docker and run it with:
make docker

The endpoint should then be available at localhost:8080