enaswan 0.1.0

ENA Smart Workflow and Acquisition Network — fast parallel FASTQ downloader for the European Nucleotide Archive

🦢 enaswan

ENA Smart Workflow and Acquisition Network

A fast, parallel command-line toolkit to fetch metadata, download FASTQ files, and verify integrity from the European Nucleotide Archive (ENA).

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Installation

Via pip (PyPI)

pip install enaswan

Via conda (Bioconda)

conda install -c bioconda enaswan

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Workflow

Run the three steps in order:

Step 1 — Fetch Metadata

enaswan --meta SRR12345678
enaswan --meta SRR12345678 ERR000001 PRJNA123456   # multiple IDs
enaswan --meta SRR12345678 --outdir ./results       # custom output folder

Saves a <ID>_metadata.csv file containing run accession, sample info, instrument model, file sizes, FTP links, and MD5 checksums.

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Step 2 — Download FASTQ Files

enaswan --dl SRR12345678
enaswan --dl SRR12345678 ERR000001                  # multiple IDs
enaswan --dl SRR12345678 --threads 8 --outdir ./data  # parallel + custom dir

• Downloads are parallel (default: 4 threads)
• Resumes interrupted downloads automatically
• Shows a real-time progress bar

📶 Note: Download speed will vary depending on your internet connection and ENA server load.

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Step 3 — Verify Integrity

enaswan --check SRR12345678_metadata.csv

Computes MD5 checksums for each downloaded file and compares against ENA's expected values. Reports PASS ✅, MISSING ⚡, or CORRUPTED ❌.

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Full Options

usage: enaswan [-h] (--meta ID [ID ...] | --dl ID [ID ...] | --check metadata.csv)
               [--threads N] [--outdir DIR]

options:
  --meta   ID [ID ...]    Fetch metadata CSV for accession IDs
  --dl     ID [ID ...]    Download FASTQ files for accession IDs
  --check  metadata.csv   Verify MD5 checksums using metadata CSV
  --threads N             Parallel download threads (default: 4)
  --outdir DIR            Output directory (default: current directory)

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Supported Accession Types

Type	Example	Description
Run	SRR*, ERR*, DRR*	Single sequencing run
Project	PRJNA*, PRJEB*	All runs in a project
Sample	SAMN*, SAME*	All runs for a sample

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License

MIT © Your Name