omicverse.alignment.fqdump

omicverse.alignment.fqdump(sra_ids, output_dir='fastq', threads=8, memory='4G', temp_dir=None, gzip=False, library_layout='auto', jobs=None, max_workers=None, retries=2, sra_dir=None, fasterq_path=None, auto_install=True, force=False)[source]

Convert SRA accessions to FASTQ.

Parameters:

  • sra_ids (Union[str, Sequence[str]]) – SRR accession (str) or list of accessions.

  • output_dir (str (default: 'fastq')) – Output directory for FASTQ files (per-sample subdir).

  • threads (int (default: 8)) – Threads per fasterq-dump job.

  • memory (str (default: '4G')) – Memory limit passed to –mem (e.g. ‘4G’).

  • temp_dir (Optional[str] (default: None)) – Temporary directory root for fasterq-dump.

  • gzip (bool (default: False)) – Compress FASTQ outputs with pigz/gzip.

  • library_layout (str (default: 'auto')) – ‘auto’, ‘single’, or ‘paired’.

  • jobs (Optional[int] (default: None)) – Concurrent jobs.

  • max_workers (Optional[int] (default: None)) – Legacy alias for jobs.

  • retries (int (default: 2)) – Retries per accession.

  • sra_dir (Optional[str] (default: None)) – Directory containing prefetched .sra/.sralite files.

  • fasterq_path (Optional[str] (default: None)) – Explicit path to fasterq-dump.

  • force (bool (default: False)) – Force overwrite existing output files (adds –force).

  • auto_install (bool (default: True)) – Install missing tools automatically when possible.

Return type:

Union[Dict[str, str], List[Dict[str, str]]]