genomerse-genomics-utils 0.1.0

Small bioinformatics utilities: VCF annotation, minimal FHIR resource validation, and a MultiQC plugin

genomics-utils

Small, focused bioinformatics utilities used as a Phase 1 portfolio package:

1. VCF annotation helper — parses a VCF file, classifies each variant (SNP / insertion / deletion / MNV), computes transition/transversion stats, and can emit a small JSON summary.
2. FHIR resource validator — structural validation of a minimal subset of FHIR R4 Patient and Observation resources.
3. MultiQC plugin — a MultiQC module that visualizes the VCF annotation summary JSON in a MultiQC report.

Installation

pip install -e ".[dev,docs]"

Components

VCF annotation helper

See genomics_utils.vcf_annotate. Operates on a small, hand-authored synthetic VCF (see tests/data/README.md) purely for demonstration and testing — it is not a production-grade annotation engine (no external annotation database lookups, no INFO/CSQ field parsing beyond what is generated locally).

FHIR resource validator

See genomics_utils.fhir_validate.

Scope note: this validator only checks that a JSON document has the shape of a minimal FHIR R4 Patient or Observation resource (required fields present, correct basic types). It does not perform full FHIR conformance validation — it does not check terminology bindings (e.g. that a code comes from a real code system), does not validate against StructureDefinition profiles, and does not check referential integrity between resources. For conformance-grade validation, use the official HL7 FHIR validator.

MultiQC plugin

See genomics_utils.multiqc_plugin.genomics_module. Registered via the multiqc.modules.v1 entry point, it looks for *_genomics_utils.json summary files (written by the VCF annotation helper) and renders variant counts and a Ts/Tv ratio in the MultiQC report.

Sample data

All test fixtures under tests/data/ are either hand-authored synthetic data or minimal official examples pulled from public specifications — see tests/data/README.md for exact provenance of each file.