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Using py‐ard from the command line

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Pradeep Bashyal edited this page Oct 2, 2023 · 1 revision

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.

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