ucsc-conservation-and-tfbs

1# Conservation Scores & TFBS Lookup (UCSC)
2 
3This skill provides access to evolutionary constraint scores and conserved
4elements from the UCSC Genome Browser. It retrieves scores from the PHAST
5package — specifically `phastCons` (identifying functional blocks) and `phyloP`
6(measuring individual site constraint) — calculated from multiple alignments.
7 
8Use this skill to determine if a non-coding variant hits a site that hasn't
9changed since a common ancestor (which is a strong signal for pathogenicity) or
10to find conservation peaks across a regulatory element.
11 
12## Prerequisites
13 
141.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
15    `uv` is installed and on PATH.
162.  **User Notification**: If .licenses/ucsc_conservation_and_tfbs_LICENSE.txt
17    does not already exist in the workspace root directory then (1) prominently
18    notify the user to check the terms at
19    https://genome.ucsc.edu/conditions.html and
20    https://genome.ucsc.edu/goldenPath/help/api.html, then (2) create the file
21    recording the notification text and timestamp.
22 
23## Core Rules
24 
25-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
26    database rather than accessing the database directly. The scripts
27    automatically enforce the required rate limit gracefully.
28-   **Large Output Handling**: Always pass --output to redirect output to a
29    file. Parse it separately (using jq or your own code).
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