4e986673a37800eacf1d36309b0cd38564a4bb1f
max
  Wed Mar 25 07:55:59 2026 -0700
PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/scripts/primateAiToBigBed.py src/hg/makeDb/scripts/primateAiToBigBed.py
deleted file mode 100644
index 4e58a7e7332..00000000000
--- src/hg/makeDb/scripts/primateAiToBigBed.py
+++ /dev/null
@@ -1,57 +0,0 @@
-#!/usr/bin/env python3
-"""
-Convert PrimateAI-3D.hg38.txt.gz to a BED file for bigBed conversion.
-Input positions are 1-based, output BED is 0-based.
-Colors: red for pathogenic, blue for benign.
-"""
-
-import gzip
-import sys
-import os
-
-INFILE = "PrimateAI-3D.hg38.txt.gz"
-OUTFILE = "primateAi.bed"
-
-def main():
-    inPath = INFILE
-    outPath = OUTFILE
-
-    print(f"Reading {inPath}...", file=sys.stderr)
-    count = 0
-    with gzip.open(inPath, "rt") as fh, open(outPath, "w") as out:
-        header = fh.readline()  # skip header
-        for line in fh:
-            fields = line.rstrip("\n").split("\t")
-            chrom = fields[0]
-            pos = int(fields[1])  # 1-based
-            ref = fields[2]
-            alt = fields[3]
-            gene = fields[4]
-            refAa = fields[6]
-            altAa = fields[7]
-            scorePai = float(fields[8])
-            percentile = float(fields[9])
-            refSeq = fields[10]
-            prediction = fields[11]
-
-            chromStart = pos - 1  # convert to 0-based
-            chromEnd = pos
-            name = f"{refAa}>{altAa}"
-            score = int(round(percentile * 1000))
-            rgb = "200,0,0" if prediction == "pathogenic" else "0,0,200"
-
-            mouseOver = f"{ref}>{alt} {name} score={scorePai:.3f} pct={percentile:.3f} ({prediction})"
-
-            out.write(f"{chrom}\t{chromStart}\t{chromEnd}\t{name}\t{score}\t"
-                       f"+\t{chromStart}\t{chromEnd}\t{rgb}\t"
-                       f"{ref}\t{alt}\t{gene}\t{refSeq}\t{scorePai:.3f}\t{percentile:.3f}\t"
-                       f"{prediction}\t{mouseOver}\n")
-            count += 1
-            if count % 10000000 == 0:
-                print(f"  {count} variants processed...", file=sys.stderr)
-
-    print(f"  {count} variants written to {outPath}", file=sys.stderr)
-    print("Done. Now sort and run bedToBigBed.", file=sys.stderr)
-
-if __name__ == "__main__":
-    main()