.. _api_models:

Data Models Module (biallelic.models)
=====================================

The models module contains all core data classes and enums for representing
genomic data in the biallelic inactivation pipeline.

.. automodule:: biallelic.models
   :members:
   :undoc-members:
   :show-inheritance:

Overview
--------

This module defines:

- **Enums** for categorical data types (Gender, OmicsType, AberrationType, DoubleHitType)
- **Classes** for representing genomic events (SampleDonor, Aberration, DoubleHit)

All classes are designed to work with the Aberrations orchestrator and discovery analyses.

Usage Examples
--------------

Creating a Sample Donor:

.. code-block:: python

    from biallelic.models import SampleDonor, Gender

    donor = SampleDonor(
        sample_id="TCGA-BL-A0C8-01A",
        donor_id="TCGA-BL-A0C8",
        gender=Gender.Female,
        cellularity=0.95,
        ploidy=2.0
    )

Creating an Aberration:

.. code-block:: python

    from biallelic.models import Aberration, AberrationType

    snv = Aberration(
        chrom="17",
        start=41196312,
        end=41196313,
        aberration_type=AberrationType.SNV,
        aberration_subtype="missense_variant",
        sample_id="TCGA-BL-A0C8-01A",
        gene="TP53",
        vaf=0.45
    )

Creating a Double Hit (Biallelic Event):

.. code-block:: python

    from biallelic.models import DoubleHit, DoubleHitType

    biallelic_hit = DoubleHit(
        gene="TP53",
        sample_id="TCGA-BL-A0C8-01A",
        hit_type=DoubleHitType.SOM_SNV_SOM_LOSS,
        hit_details="SNV at codon 248 + loss of chr17"
    )

See Also
--------

- :ref:`manifest`: Configuration file format for analyses
- :ref:`developing`: Guide for extending the package