Validating PMOs pmotools-python

pmotools-python validate_pmo

Can download multiple PMOs here

https://plasmogenepi.github.io/PMO_Docs/format/moz2018_PMO.json.gz

https://plasmogenepi.github.io/PMO_Docs/format/PathWeaverHeome1_PMO.json.gz

Code

pmotools-python validate_pmo --help

usage: pmotools-python validate_pmo [-h] --pmo PMO
                                    [--jsonschema_version JSONSCHEMA_VERSION]
                                    [--jsonschema_file JSONSCHEMA_FILE]

Validate a PMO file against a JSON Schema

options:
  -h, --help            show this help message and exit
  --pmo PMO             a pmo file to validate
  --jsonschema_version JSONSCHEMA_VERSION
                        version of the jsonschema to validate against
                        (default: 1.1.0)
  --jsonschema_file JSONSCHEMA_FILE
                        explicit jsonschema file path to validate against
                        (overrides --jsonschema_version)

Use this validate a PMO file that follows the standard format, by default will use the schema that is within the pmotools-python directory

Code

cd example 

wget https://plasmogenepi.github.io/PMO_Docs/format/moz2018_PMO.json.gz


pmotools-python validate_pmo --pmo moz2018_PMO.json.gz

Can also use specific jsonschema file

Code

cd example 

wget https://plasmogenepi.github.io/PMO_Docs/format/moz2018_PMO.json.gz
wget https://plasmogenepi.github.io/PMO_Docs/format/portable_microhaplotype_object.schema.json


pmotools-python validate_pmo --pmo moz2018_PMO.json.gz --jsonschema_file portable_microhaplotype_object.schema.json

The python code for validate_pmo script is below

Code

pmotools-python/src/pmotools/scripts/pmo_utils/validate_pmo.py

#!/usr/bin/env python3
import os
import argparse
import json


from pmotools.pmo_engine.pmo_reader import PMOReader
from pmotools.pmo_engine.pmo_checker import PMOChecker
from pmotools.utils.small_utils import Utils
from pmotools import __version__ as __pmotools_version__


def get_parser_validate_pmo() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(
        prog="pmotools-python validate_pmo",
        description="Validate a PMO file against a JSON Schema",
    )
    parser.add_argument("--pmo", type=str, required=True, help="a pmo file to validate")
    parser.add_argument(
        "--jsonschema_version",
        default=__pmotools_version__,
        type=str,
        required=False,
        help="version of the jsonschema to validate against (default: %(default)s)",
    )
    parser.add_argument(
        "--jsonschema_file",
        default=None,
        type=str,
        required=False,
        help="explicit jsonschema file path to validate against (overrides --jsonschema_version)",
    )
    return parser


def parse_args_validate_pmo():
    parser = get_parser_validate_pmo()
    args = parser.parse_args()

    # post-parse resolution stays here, NOT in get_parser
    if args.jsonschema_file is None:
        args.jsonschema_file = os.path.join(
            os.path.dirname(
                os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
            ),
            "schemas/",
            f"portable_microhaplotype_object_v{args.jsonschema_version}.schema.json",
        )
    return args


def validate_pmo():
    args = parse_args_validate_pmo()

    # read in the PMO
    pmo = PMOReader.read_in_pmo(args.pmo)

    # create checker
    with Utils.smart_open_read_by_ext(args.jsonschema_file) as f:
        checker = PMOChecker(json.load(f))
        # validate
        checker.validate_pmo_json(pmo)


if __name__ == "__main__":
    validate_pmo()