CLI Reference¶
The Custom Panel command-line interface provides powerful tools for gene panel curation and management.
Overview¶
The CLI is built with Typer and provides several main commands:
run- Execute the complete gene panel pipelinefetch- Fetch data from individual sourcesconfig-check- Validate configuration filessearch-panels- Search available panels in PanelApp
Main Module¶
custom_panel.cli ¶
Improved command-line interface for the custom-panel tool.
This module provides the main CLI commands using Typer with better modularization and use of the new utilities.
config_check ¶
Validate and display configuration using improved config management.
display_summary ¶
Display pipeline summary statistics using improved utilities.
fetch ¶
fetch(source=typer.Argument(..., help='This command is deprecated.'), config_file=typer.Option(None, '--config-file', '-c', help='Configuration file path'), output_dir=typer.Option('results/fetch', '--output-dir', '-o', help='Output directory'), format=typer.Option('parquet', '--format', '-f', help='Output format (parquet, csv, excel)'), log_level=typer.Option('INFO', '--log-level', help='Log level'))
(DEPRECATED) Fetch data from a single source. Please use the 'run' command instead.
load_config_manager ¶
Load configuration from files and create a ConfigManager instance.
run ¶
run(config_file=typer.Option(None, '--config-file', '-c', help='Configuration file path'), output_dir=typer.Option(None, '--output-dir', '-o', help='Output directory'), score_threshold=typer.Option(None, '--score-threshold', help='Override the evidence score threshold for gene inclusion'), log_level=typer.Option('INFO', '--log-level', help='Log level (DEBUG, INFO, WARNING, ERROR)'), dry_run=typer.Option(False, '--dry-run', help='Run without generating output files'), save_intermediate=typer.Option(False, '--save-intermediate', help='Save intermediate files for debugging'), intermediate_format=typer.Option(None, '--intermediate-format', help='Format for intermediate files (csv, excel, parquet, json)'), log_to_file=typer.Option(False, '--log-to-file', help='Save logs to files'), structured_output=typer.Option(True, '--structured-output/--flat-output', help='Use structured output directories'))
Run the complete gene panel curation pipeline.
search_panels ¶
search_panels(query=typer.Argument(..., help='Search term for panel names'), config_file=typer.Option(None, '--config-file', '-c', help='Configuration file path'), log_level=typer.Option('INFO', '--log-level', help='Log level'))
Search for available panels in PanelApp.