plasmidsaurus

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:*)

Plasmidsaurus CLI

Fetch sequencing data from the Plasmidsaurus API.

Prerequisites

Requires environment variables (already configured in ~/.zshrc):

• PLASMIDSAURUS_CLIENT_ID
• PLASMIDSAURUS_CLIENT_SECRET

Always source ~/.zshrc before running commands:

source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py <command>

Commands

List Orders

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 JSON

Item Info

Get detailed information about a specific order:

source ~/.zshrc && python3 scripts/plasmidsaurus_cli.py info <item_code>

Options:

• --json: Output as JSON

Download Results

Download 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 extraction

Downloads are saved to <output_dir>/<item_code>/ with subdirectories:

• results/: Assembled sequences, annotations, maps
• reads/: Raw sequencing reads

Auto-Fetch New Results

Automatically 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

Examples

# 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