gbanyan
ee27f3ad2f
- load_to_duckdb: Saves constraint DataFrame to gnomad_constraint table with provenance tracking - query_constrained_genes: Queries constrained genes by LOEUF threshold (validates GCON-03 interpretation) - evidence_cmd.py: CLI command group with gnomad subcommand (fetch->transform->load orchestration) - Checkpoint-restart: Skips processing if gnomad_constraint table exists (--force to override) - Full CLI: usher-pipeline evidence gnomad [--force] [--url URL] [--min-depth N] [--min-cds-pct N]
106 lines
3.1 KiB
Python
106 lines
3.1 KiB
Python
"""Main CLI entry point for usher-pipeline.
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Provides command group with global options and subcommands for pipeline operations.
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"""
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import logging
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from pathlib import Path
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import click
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from usher_pipeline import __version__
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from usher_pipeline.config.loader import load_config
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from usher_pipeline.cli.setup_cmd import setup
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from usher_pipeline.cli.evidence_cmd import evidence
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# Configure logging
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logging.basicConfig(
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level=logging.INFO,
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format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
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)
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@click.group()
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@click.option(
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'--config',
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type=click.Path(exists=True, path_type=Path),
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default='config/default.yaml',
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help='Path to pipeline configuration YAML file'
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)
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@click.option(
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'--verbose',
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is_flag=True,
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help='Enable verbose logging (DEBUG level)'
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)
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@click.pass_context
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def cli(ctx, config, verbose):
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"""Usher-pipeline: Reproducible pipeline for discovering under-studied cilia/Usher candidate genes.
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Provides data infrastructure, gene ID mapping, evidence layer aggregation,
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and scoring for candidate gene prioritization.
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"""
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# Set up context
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ctx.ensure_object(dict)
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ctx.obj['config_path'] = config
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ctx.obj['verbose'] = verbose
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# Set logging level
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if verbose:
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logging.getLogger().setLevel(logging.DEBUG)
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logging.debug("Verbose logging enabled")
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@cli.command()
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@click.pass_context
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def info(ctx):
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"""Display pipeline information and configuration summary."""
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config_path = ctx.obj['config_path']
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click.echo(f"Usher Pipeline v{__version__}")
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click.echo(f"Config: {config_path}")
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click.echo()
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try:
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config = load_config(config_path)
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# Display config hash
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config_hash = config.config_hash()
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click.echo(f"Config Hash: {config_hash[:16]}...")
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click.echo()
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# Display data source versions
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click.echo(click.style("Data Source Versions:", bold=True))
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click.echo(f" Ensembl Release: {config.versions.ensembl_release}")
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click.echo(f" gnomAD Version: {config.versions.gnomad_version}")
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click.echo(f" GTEx Version: {config.versions.gtex_version}")
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click.echo(f" HPA Version: {config.versions.hpa_version}")
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click.echo()
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# Display paths
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click.echo(click.style("Paths:", bold=True))
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click.echo(f" Data Directory: {config.data_dir}")
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click.echo(f" Cache Directory: {config.cache_dir}")
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click.echo(f" DuckDB Path: {config.duckdb_path}")
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click.echo()
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# Display API config
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click.echo(click.style("API Configuration:", bold=True))
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click.echo(f" Rate Limit: {config.api.rate_limit_per_second} req/s")
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click.echo(f" Max Retries: {config.api.max_retries}")
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click.echo(f" Cache TTL: {config.api.cache_ttl_seconds}s")
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click.echo(f" Timeout: {config.api.timeout_seconds}s")
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except Exception as e:
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click.echo(click.style(f"Error loading config: {e}", fg='red'), err=True)
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ctx.exit(1)
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# Register commands
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cli.add_command(setup)
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cli.add_command(evidence)
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if __name__ == '__main__':
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cli()
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