59e0ac66496c36893df2b1440a037557fed23ff4
max
  Mon Mar 23 04:31:33 2026 -0700
fixing up primateai makedoc, refs #37274

diff --git src/hg/makeDb/scripts/primateai/primateAiToBigBed.py src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
new file mode 100644
index 00000000000..4e58a7e7332
--- /dev/null
+++ src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
@@ -0,0 +1,57 @@
+#!/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()