a56d88e05670b759ff3b32829542537ccc790c57
lrnassar
  Tue Apr 28 19:18:20 2026 -0700
Address CR feedback on insight + tp53 hub scripts. refs #37418

Drop duplicated bash() wrappers in favor of subprocess.run / check_output
with list args, eliminating shell=True, embedded-quote concerns, and
stderr-into-stdout merging. Centralize common operations as
run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed.

Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors
mouseover (previously unescaped) now escapes HGVS fields, addressing the
specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with
<br> across all five affected mouseover sites.

diff --git src/hg/makeDb/scripts/tp53/tp53FuncPrelim.py src/hg/makeDb/scripts/tp53/tp53FuncPrelim.py
index 844f0538dad..c66b4395779 100644
--- src/hg/makeDb/scripts/tp53/tp53FuncPrelim.py
+++ src/hg/makeDb/scripts/tp53/tp53FuncPrelim.py
@@ -179,31 +179,31 @@
     variants = load_variants(src_xlsx)
     print("  {} missense variants".format(len(variants)))
     from collections import Counter
     print("  Distribution: {}".format(Counter(v['code'] for v in variants)))
     raw_scores = lib.load_per_paper_raw_scores()
     print("  Per-paper raw-score lookup: {} unique missense changes".format(
         len(raw_scores)))
     bed_lines = generate_bed(variants, tx, raw_scores)
     print("  {} BED rows".format(len(bed_lines)))
 
     as_file = os.path.join(outdir, "TP53FuncPrelim.as")
     lib.write_autosql(as_file, AUTOSQL)
     bed = os.path.join(outdir, "TP53FuncPrelim_{}.bed".format(db))
     with open(bed, 'w') as f:
         f.write("\n".join(bed_lines) + "\n")
-    lib.bash("sort -k1,1 -k2,2n {0} -o {0}".format(bed))
+    lib.run_sort_bed(bed)
     bb = os.path.join(outdir, "TP53FuncPrelim{}.bb".format(db.capitalize()))
     lib.run_bedToBigBed(bed, as_file, bb, lib.chrom_sizes_path(db), "bed9+7")
     print("  wrote {}".format(bb))
 
 
 def main():
     p = argparse.ArgumentParser(description=__doc__)
     p.add_argument('-o', '--output-dir', default=DEFAULT_OUTDIR)
     p.add_argument('--db', action='append', help='hg38 or hg19 (repeat). Default hg38.')
     p.add_argument('--src', default=DEFAULT_SRC)
     args = p.parse_args()
     dbs = args.db if args.db else ['hg38']
     for db in dbs:
         build(db, args.output_dir, args.src)