Conservation Scores & TFBS Lookup (UCSC)

This skill provides access to evolutionary constraint scores and conserved elements from the UCSC Genome Browser. It retrieves scores from the PHAST package, specifically phastCons (identifying functional blocks) and phyloP (measuring individual site constraint), calculated from multiple alignments.

Use this skill to determine if a non-coding variant hits a site that hasn't changed since a common ancestor (which is a strong signal for pathogenicity) or to find conservation peaks across a regulatory element.

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/ucsc_conservation_and_tfbs_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://genome.ucsc.edu/conditions.html and https://genome.ucsc.edu/goldenPath/help/api.html, then (2) create the file recording the notification text and timestamp.

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.
• Large Output Handling: Always pass --output to redirect output to a file. Parse it separately (using jq or your own code).
• Notification: If this skill is used, ensure this is mentioned in the output.

Utility Scripts

This skill includes scripts to query different types of genomic data from UCSC:

1. scripts/get_conservation.py: For Evolutionary Conservation scores (phyloP, phastCons).
2. scripts/get_tfbs.py: For Transcription Factor Binding Sites (TFBS).
3. scripts/list_tracks.py: For listing available tracks based on search or group constraints.