controlled-vocabulary-utils 0.3.0

Usage

Contents of the controlled vocabulary configuration file:

---
format_version: 0.1.0
name: Controlled Vocabulary for Bioinformatics
description: TBD
terms:
  - name: variant_effect_on_function
    def: The effect that the variant has on the function of the gene.
    datatype: string
    accepted_values:
      "loss": The variant has caused a loss of function.
      "gain": The variant has caused a gain of function.
  - name: region_of_transcript_affected
    def: The region of the transcript that the variant affects.
    datatype: string
    accepted_values:
      "start": The variant affects the start of the transcript.
      "end": The variant affects the end of the transcript.
      "whole transcript": The variant affects the whole transcript.
      "overlapping end": The variant overlaps one end of the ends of the transcript.
  - name: variant_status
    def: TBD
    alt_names:
      - variant_qc_status
    datatype: string
    accepted_values:
  - name: score
    def: TBD
    datatype: integer
    accepted_values:
      "10": "very low score"
      "20": "low score"
      "40": "mid-level score"
  - name: zygosity
    def: TBD
    alt_names:
      - zyg
    datatype: string
    accepted_values:
      "heterozygous": "heterozygous"
      "homozygous": "homozygous"
      "mosaic": "mosaic"

from controlled_vocabulary_utils import CVValidationManager

config_file = "conf/controlled_vocabulary.yaml"

vm = ValidationManager(
    config_file=config_file,
    verbose=verbose,
)

term = "zygosity"
val = "mosaic"
if vm.is_valid(term, val):
    print(f"'{val}' is a valid value for term '{term}'")
else:
    print(f"'{val}' is NOT a valid value for term '{term}'")