Instruction file imported from murphycj/AGFusion (.github/instructions/python.instructions.md). Copyright stays with the author.

AGFusion Python Guidelines

Name: python
Author: murphycj

Code Style

Format all Python code with black (line-length = 100)
Target Python 3.9 - 3.13
Run black . before committing

Module Responsibilities

Module	Purpose
`agfusion/model.py`	Core domain classes: `_Gene`, `Fusion`. Holds exon/protein architecture logic.
`agfusion/database.py`	`AGFusionDB` — SQLite-backed store of protein domain annotations (Pfam, TMHMM, etc.)
`agfusion/parsers.py`	Parsers for fusion-finding algorithm output files (one parser per algorithm)
`agfusion/plot.py`	Matplotlib-based visualization of protein domain and exon structures
`agfusion/cli.py`	Click-based CLI entry points: `annotate`, `batch`, `download`
`agfusion/utils.py`	Shared utility functions
`agfusion/exceptions.py`	Custom exception classes

Python Conventions

Protein database annotation keys: "pfam", "tmhmm", etc.
pyensembl.EnsemblRelease objects provide transcript/exon lookups
Add new fusion-finding parsers to parsers.py — one parser per algorithm

Testing

Tests use unittest.TestCase in test/
Tests require local AGFusion .db files and pyensembl data installed
Add new test cases to test_base.py, test_parsers.py, or test_plots.py as appropriate
Run tests with: python -m pytest test/

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AGFusion Python Guidelines

Code Style

Module Responsibilities

Python Conventions

Testing

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