trait2gene

trait2gene is a Python package and CLI for end-to-end PoPS-style GWAS gene prioritization. It standardizes config validation, resource resolution, MAGMA handoff, feature preparation, PoPS execution, locus-level ranking, and report generation behind one reproducible workflow.

Getting Started

• Installation
  • Runtime install
  • Documentation install
  • External dependencies
  • Public example without local MAGMA
• Quickstart
  • Minimal validation flow
  • Full-run templates
  • Standard pipeline order
  • Public example

Guides

• Architecture
  • Core responsibilities
  • Execution model
  • Package layout
  • Why the stages stay separate
• CLI Guide
  • Main commands
  • Recommended full-run flow
  • Precomputed MAGMA flow
  • doctor
  • inspect outputs
• Configuration Guide
  • Minimum required fields
  • Example templates
  • Common path fields
  • Prefix semantics
  • Modes
  • Upstream-aligned defaults
• Output Layout
  • Top-level layout
  • What each section contains
  • Why this layout matters

Tutorials

• Tutorials
  • Tutorial: Real Paths and End-to-End Runs
  • Tutorial: Public Schizophrenia Example

Reference

• API Reference
  • trait2gene.cli
  • trait2gene.config.loader
  • trait2gene.config.models
  • trait2gene.engine.runner
  • trait2gene.engine.plan
  • trait2gene.examples.public_schizophrenia
  • trait2gene.resources.resolver
  • trait2gene.workflows.validate
  • trait2gene.workflows.prepare
  • trait2gene.workflows.magma_stage
  • trait2gene.workflows.feature_stage
  • trait2gene.workflows.pops_stage
  • trait2gene.workflows.prioritize_stage
  • trait2gene.workflows.report_stage
  • trait2gene.workflows.doctor

Highlights

• External MAGMA execution without redistributing MAGMA itself

• Upstream-compatible PoPS wrapping with standardized intermediate outputs

• Strict YAML configuration via Pydantic models

• Locus prioritization and HTML reporting on top of PoPS outputs

• Reproducible public example using real downloaded data

Real public example

The repository includes a full public schizophrenia walkthrough. It downloads public inputs, writes a machine-local config, runs the pipeline using precomputed MAGMA outputs, and verifies that trait2gene reproduces the public upstream PoPS results.

python scripts/run_public_schizophrenia_example.py

Key artifacts:

• real_runs/schizophrenia_public_example/results/reports/report.html

• real_runs/schizophrenia_public_example/verification_summary.json

• real_runs/schizophrenia_public_example/result_snapshot.json