| 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
download-flatfile BCT VRL
download-flatfile -https PLN INV
download-flatfile -verify BCT VRL
Recommended Workflow
- Start in a dedicated download directory because all
.seq.gz files are written to the current working directory.
- Download the divisions you need, choosing
-https if FTP is flaky in your environment.
- Re-run with
-verify before downstream processing when download integrity matters.
- 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.
