download-flatfile

name	download-flatfile
description	Use when mirroring consolidated NCBI GenBank flatfile divisions into the current directory or verifying existing downloaded flatfiles.
disable-model-invocation	true
user-invocable	true

download-flatfile

Quick Start

• Command: download-flatfile [-ftp|-https] [-verify] division...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/download-flatfile
• Full reference: See references/help.md

When To Use This Tool

• Download one or more GenBank flatfile divisions as .seq.gz archives.
• Re-check previously downloaded GenBank flatfiles and remove corrupt or empty files with -verify.
• Build a local flatfile mirror for downstream XML conversion or archive indexing.

Common Patterns

# 1) Download bacterial and viral GenBank flatfiles via the default FTP mode
download-flatfile BCT VRL

# 2) Use HTTPS explicitly if FTP routing is unreliable
download-flatfile -https PLN INV

# 3) Validate existing flatfiles and delete broken or empty downloads
download-flatfile -verify BCT VRL

Recommended Workflow

1. Start in a dedicated download directory because all .seq.gz files are written to the current working directory.
2. Download the divisions you need, choosing -https if FTP is flaky in your environment.
3. Re-run with -verify before downstream processing when download integrity matters.
4. Convert or inspect the flatfiles only after the validation pass is clean.

Guardrails

• -verify is destructive by design: it removes empty or invalid .seq.gz files so they can be re-downloaded.
• The local wrapper validates content by decompressing and checking parsed records, so verification can be expensive on large downloads.
• Output is written into the current directory, and large GenBank divisions consume substantial disk space.
• The wrapper retries failed downloads, but persistent network or content failures still leave you with deleted files that must be fetched again later.