NCBI Sequence Fetch

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/ncbi_sequence_fetch_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ncbi.nlm.nih.gov/ and https://www.ncbi.nlm.nih.gov/home/about/policies/, then (2) create the file recording the notification text and timestamp.
3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist.
4. NCBI_API_KEY (optional): Raises the NCBI rate limit from 3 to 10 requests/second. The skill works without it, but a key is recommended if the user plans many queries or encounters a 429 error. You can register for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You MUST use the safe credentials protocol in the credentials skill to check for and request this key if this skill looks relevant to the user's request.

Core Rules

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
• API Key Support: If the user provides an NCBI_API_KEY in their environment, the query speed limits are automatically increased significantly.
• Notification: If this skill is used, ensure this is mentioned in the output.

Overview

Wraps NCBI's Entrez E-utilities (efetch, esearch, elink, esummary) for retrieving protein and nucleotide sequences. Provides 10 subcommands covering the full range of sequence retrieval workflows: