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Fetch Sra

Summary

Download SRA run FASTQ files and optional XML metadata from ENA

Description

Takes either a single SRA run ID (e.g., SRR12345678) or a file containing multiple run IDs (one per line). Downloads FASTQ files and optionally XML metadata reports to the specified output directory.

Example usage:


# Download single run:
rolypoly fetch-sra -i SRR12345678 -o output_dir

# Download multiple runs with metadata:
rolypoly fetch-sra -i run_ids.txt -o output_dir --report

* Note: The fastq headers may vary for the same SRA run/expriemtn based on the source and fetching method (s3, ftp, ena...)

Usage

rolypoly fetch-sra [OPTIONS]

Options

  • -i, --input: SRA run ID or file containing run IDs (one per line) (type: TEXT; required; default: Sentinel.UNSET)
  • -o, --output-dir: Directory to save downloaded files (type: DIRECTORY; default: ./)
  • --report: Download XML report for each run (type: BOOLEAN; default: False)