omicverse.alignment.prefetch¶
- omicverse.alignment.prefetch(sra_ids, output_dir='prefetch', threads=4, jobs=None, max_workers=None, retries=2, validate=True, transport=None, location=None, prefetch_path=None, vdb_validate_path=None, link_mode='symlink', auto_install=True, progress_minutes=1, force=None)[source]¶
Prefetch SRA accessions with validation.
- Parameters:
sra_ids (
Union[str,Sequence[str]]) – SRR accession (str) or list of accessions.output_dir (
str(default:'prefetch')) – Output directory for downloaded .sra/.sralite files.threads (
int(default:4)) – Default concurrency when jobs is not provided (kept for compatibility).jobs (
Optional[int] (default:None)) – Number of concurrent downloads (preferred).max_workers (
Optional[int] (default:None)) – Legacy alias for jobs.retries (
int(default:2)) – Retries per accession.validate (
bool(default:True)) – Run vdb-validate on the downloaded file.transport (
Optional[str] (default:None)) – Optional prefetch –transport value (e.g. ‘https’).location (
Optional[str] (default:None)) – Optional prefetch –location value (e.g. ‘ncbi’, ‘ena’).prefetch_path (
Optional[str] (default:None)) – Explicit path to prefetch executable.vdb_validate_path (
Optional[str] (default:None)) – Explicit path to vdb-validate executable.link_mode (
str(default:'symlink')) – symlink, hardlink, or copy (fallback).auto_install (
bool(default:True)) – Install missing tools automatically when possible.progress_minutes (
int(default:1)) – Prefetch progress interval in minutes (0 disables progress).force (
Optional[str] (default:None)) – Optional prefetch force mode: “no”, “yes”, or “all”.
- Return type: