ga4gh2studio 0.2.0

Convert GA4GH Pedigree Standard and Phenopackets to Pedigree Studio session JSON

ga4gh2studio

Convert GA4GH Pedigree Standard and Phenopackets Family files into Pedigree Studio session JSON.

The reverse complement of studio2ga4gh. Together they provide bidirectional interoperability between Pedigree Studio and the GA4GH ecosystem.

Installation

pip install ga4gh2studio

Usage

Command line

# From GA4GH Pedigree only
ga4gh2studio -g pedigree_ga4gh.json -o session.json

# From Phenopackets Family only
ga4gh2studio -p family_phenopackets.json -o session.json

# From both (GA4GH for structure, Phenopackets for disease labels)
ga4gh2studio -g pedigree_ga4gh.json -p family_phenopackets.json -o session.json

Python API

import ga4gh2studio, json

# From GA4GH Pedigree
with open("pedigree_ga4gh.json") as f:
    ga4gh = json.load(f)
result = ga4gh2studio.convert(ga4gh_data=ga4gh)
with open("session.json", "w") as f:
    json.dump(result.session, f, indent=2)

# From both sources
with open("family_phenopackets.json") as f:
    pp = json.load(f)
result = ga4gh2studio.convert(ga4gh_data=ga4gh, phenopackets_data=pp)
print(result.summary)

Input Handling

Input	What it provides
GA4GH Pedigree only	Full structure: parent-child (biological + adoptive), twins, sex, deceased status, proband
Phenopackets Family only	PED-compatible structure (parents, sex, affected status) + disease labels
Both (recommended)	GA4GH provides rich structure; Phenopackets enriches with disease names and vital status

Feature Mapping

GA4GH / Phenopackets	Pedigree Studio
KIN:027 isBiologicalMotherOf	Partnership + solid child link
KIN:028 isBiologicalFatherOf	Partnership + solid child link
KIN:022 isAdoptiveParentOf	Partnership + dashed child link
KIN:010 isMonozygoticTwin	Identical twin link
KIN:011 isDizygoticTwin	Non-identical twin link
indexPatients	Proband arrow
Individual.deceased	Deceased diagonal line
Individual.name / dateOfBirth	Annotation text ("Name\nb. 1985")
Disease term labels	Legend entries with distinct colours
Shared ancestors	Consanguineous partnership (double line)

License

MIT