refgenie

import refgenie import os # Initialize RefgenieClient. It will look for ~/.refgenie/refgenie.yaml by default. # For a temporary or custom config, provide the path. # If no config is found at the default path, an empty client is initialized. # For this example, we'll try to use a default or an empty one. # Create a dummy refgenie.yaml for demonstration if it doesn't exist config_path = os.path.expanduser("~/.refgenie/refgenie.yaml") if not os.path.exists(os.path.dirname(config_path)): os.makedirs(os.path.dirname(config_path)) if not os.path.exists(config_path): with open(config_path, 'w') as f: f.write("refgenie:\n genome_config_version: 0.2\n genomes: {}\n") rg = refgenie.RefgenieClient(config_file=config_path) print(f"Refgenie client initialized. Config file: {rg.config_file}") # List available genomes (will be empty if no assets are pulled) genomes = rg.list_genomes() print(f"Available genomes: {list(genomes.keys())}") # Example: trying to get an asset (will likely fail if not pulled/built) # To make this runnable without pre-pulled assets, we'll skip direct asset retrieval # Try to get a non-existent asset to show expected behavior without erroring try: # This assumes 'human_genome' is a valid genome and 'fasta' is an asset for it # For a real scenario, you would run `refgenie pull human_genome/fasta` first # or build your own assets. # asset_path = rg.get_asset("human_genome/fasta") # print(f"Path to human_genome fasta: {asset_path}") print("To get an asset, first ensure it's pulled or built locally.") print("Example: 'refgenie pull hg38/fasta' from command line.") except Exception as e: print(f"Could not retrieve asset (expected if not pulled): {e}") # Clean up dummy config for demonstration # os.remove(config_path) # os.rmdir(os.path.dirname(config_path)) # Only if directory is empty