AgentSkillsCN

plasmidsaurus

从 Plasmidsaurus 获取测序数据。适用于用户询问如何列出测序订单、下载测序结果、查询订单状态，或从 Plasmidsaurus 检索质粒序列时使用。

SKILL.md
--- frontmatter
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:*), Bash(python3:*)

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:

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

Commands

List Orders

List all sequencing orders:

bash
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:

bash
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:

bash
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:

bash
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

bash
# 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