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Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
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| name | plasmidsaurus |
| description | Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus. |
| allowed-tools | Bash(plasmidsaurus_cli:*) |
Fetch sequencing data from the Plasmidsaurus API.
Requires environment variables (already configured in ~/.zshrc):
PLASMIDSAURUS_CLIENT_IDPLASMIDSAURUS_CLIENT_SECRETAlways source ~/.zshrc before running commands:
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py <command>
List all sequencing orders:
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py list
Options:
--status {complete,processing,pending}: Filter by status--no-shared: Exclude shared items--json: Output as JSONGet detailed information about a specific order:
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py info <item_code>
Options:
--json: Output as JSONDownload sequencing results and reads for a specific order:
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py download <item_code>
Options:
-o, --output DIR: Output directory (default: ./plasmidsaurus_data)-q, --quiet: Suppress progress output--keep-zip: Keep zip files after extractionDownloads are saved to <output_dir>/<item_code>/ with subdirectories:
results/: Assembled sequences, annotations, mapsreads/: Raw sequencing readsAutomatically download all new completed results:
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py auto-fetch
Options:
-o, --output DIR: Output directory (default: ./plasmidsaurus_data)--after DATE: Only download items completed after date (YYYY-MM-DD)--limit N: Max items to download per run (default: 5)-q, --quiet: Suppress progress output--keep-zip: Keep zip files after extraction# List all completed orders
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py list --status complete
# Get info for a specific order
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py info 8WGZXW
# Download results for an order
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py download 8WGZXW -o ./seq_data
# Auto-fetch results from the last month
source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py auto-fetch --after 2025-01-01
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