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Zhongwei Li
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skills/cosmic-database/scripts/download_cosmic.py
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231
skills/cosmic-database/scripts/download_cosmic.py
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#!/usr/bin/env python3
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"""
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COSMIC Data Download Utility
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This script provides functions to download data from the COSMIC database
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(Catalogue of Somatic Mutations in Cancer).
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Usage:
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from download_cosmic import download_cosmic_file, list_available_files
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# Download a specific file
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download_cosmic_file(
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email="user@example.com",
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password="password",
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filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz",
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output_filename="mutations.tsv.gz"
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)
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Requirements:
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- requests library: pip install requests
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- Valid COSMIC account credentials (register at cancer.sanger.ac.uk/cosmic)
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"""
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import requests
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import sys
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import os
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from typing import Optional
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def download_cosmic_file(
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email: str,
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password: str,
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filepath: str,
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output_filename: Optional[str] = None,
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genome_assembly: str = "GRCh38"
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) -> bool:
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"""
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Download a file from COSMIC database.
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Args:
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email: COSMIC account email
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password: COSMIC account password
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filepath: Relative path to file (e.g., "GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz")
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output_filename: Optional custom output filename (default: last part of filepath)
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genome_assembly: Genome assembly version (GRCh37 or GRCh38, default: GRCh38)
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Returns:
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True if download successful, False otherwise
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Example:
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download_cosmic_file(
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"user@email.com",
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"pass123",
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"GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
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)
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"""
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base_url = "https://cancer.sanger.ac.uk/cosmic/file_download/"
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# Determine output filename
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if output_filename is None:
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output_filename = os.path.basename(filepath)
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try:
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# Step 1: Get the download URL
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print(f"Requesting download URL for: {filepath}")
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r = requests.get(
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base_url + filepath,
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auth=(email, password),
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timeout=30
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)
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if r.status_code == 401:
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print("ERROR: Authentication failed. Check email and password.")
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return False
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elif r.status_code == 404:
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print(f"ERROR: File not found: {filepath}")
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return False
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elif r.status_code != 200:
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print(f"ERROR: Request failed with status code {r.status_code}")
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print(f"Response: {r.text}")
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return False
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# Parse response to get download URL
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response_data = r.json()
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download_url = response_data.get("url")
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if not download_url:
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print("ERROR: No download URL in response")
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return False
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# Step 2: Download the file
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print(f"Downloading file from: {download_url}")
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file_response = requests.get(download_url, stream=True, timeout=300)
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if file_response.status_code != 200:
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print(f"ERROR: Download failed with status code {file_response.status_code}")
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return False
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# Step 3: Write to disk
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print(f"Saving to: {output_filename}")
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total_size = int(file_response.headers.get('content-length', 0))
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with open(output_filename, 'wb') as f:
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if total_size == 0:
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f.write(file_response.content)
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else:
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downloaded = 0
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for chunk in file_response.iter_content(chunk_size=8192):
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if chunk:
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f.write(chunk)
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downloaded += len(chunk)
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# Show progress
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progress = (downloaded / total_size) * 100
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print(f"\rProgress: {progress:.1f}%", end='', flush=True)
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print() # New line after progress
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print(f"✓ Successfully downloaded: {output_filename}")
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return True
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except requests.exceptions.Timeout:
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print("ERROR: Request timed out")
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return False
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except requests.exceptions.RequestException as e:
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print(f"ERROR: Request failed: {e}")
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return False
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except Exception as e:
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print(f"ERROR: Unexpected error: {e}")
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return False
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def get_common_file_path(
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data_type: str,
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genome_assembly: str = "GRCh38",
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version: str = "latest"
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) -> Optional[str]:
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"""
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Get the filepath for common COSMIC data files.
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Args:
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data_type: Type of data (e.g., 'mutations', 'gene_census', 'signatures')
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genome_assembly: GRCh37 or GRCh38
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version: COSMIC version (use 'latest' for most recent)
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Returns:
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Filepath string or None if type unknown
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"""
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common_files = {
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'mutations': f'{genome_assembly}/cosmic/{version}/CosmicMutantExport.tsv.gz',
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'mutations_vcf': f'{genome_assembly}/cosmic/{version}/VCF/CosmicCodingMuts.vcf.gz',
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'gene_census': f'{genome_assembly}/cosmic/{version}/cancer_gene_census.csv',
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'resistance_mutations': f'{genome_assembly}/cosmic/{version}/CosmicResistanceMutations.tsv.gz',
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'structural_variants': f'{genome_assembly}/cosmic/{version}/CosmicStructExport.tsv.gz',
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'gene_expression': f'{genome_assembly}/cosmic/{version}/CosmicCompleteGeneExpression.tsv.gz',
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'copy_number': f'{genome_assembly}/cosmic/{version}/CosmicCompleteCNA.tsv.gz',
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'fusion_genes': f'{genome_assembly}/cosmic/{version}/CosmicFusionExport.tsv.gz',
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'signatures': f'signatures/signatures.tsv',
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'sample_info': f'{genome_assembly}/cosmic/{version}/CosmicSample.tsv.gz',
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}
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return common_files.get(data_type)
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def main():
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"""Command-line interface for downloading COSMIC files."""
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import argparse
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parser = argparse.ArgumentParser(
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description='Download files from COSMIC database',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Download mutations file
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%(prog)s user@email.com --filepath GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz
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# Download using shorthand
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%(prog)s user@email.com --data-type mutations
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# Download for GRCh37
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%(prog)s user@email.com --data-type gene_census --assembly GRCh37
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"""
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)
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parser.add_argument('email', help='COSMIC account email')
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parser.add_argument('--password', help='COSMIC account password (will prompt if not provided)')
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parser.add_argument('--filepath', help='Full filepath to download')
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parser.add_argument('--data-type',
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choices=['mutations', 'mutations_vcf', 'gene_census', 'resistance_mutations',
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'structural_variants', 'gene_expression', 'copy_number',
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'fusion_genes', 'signatures', 'sample_info'],
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help='Common data type shorthand')
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parser.add_argument('--assembly', default='GRCh38',
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choices=['GRCh37', 'GRCh38'],
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help='Genome assembly (default: GRCh38)')
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parser.add_argument('--version', default='latest',
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help='COSMIC version (default: latest)')
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parser.add_argument('-o', '--output', help='Output filename')
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args = parser.parse_args()
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# Get password if not provided
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if not args.password:
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import getpass
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args.password = getpass.getpass('COSMIC password: ')
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# Determine filepath
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if args.filepath:
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filepath = args.filepath
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elif args.data_type:
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filepath = get_common_file_path(args.data_type, args.assembly, args.version)
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if not filepath:
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print(f"ERROR: Unknown data type: {args.data_type}")
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return 1
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else:
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print("ERROR: Must provide either --filepath or --data-type")
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parser.print_help()
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return 1
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# Download the file
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success = download_cosmic_file(
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email=args.email,
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password=args.password,
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filepath=filepath,
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output_filename=args.output,
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genome_assembly=args.assembly
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)
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return 0 if success else 1
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if __name__ == '__main__':
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sys.exit(main())
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