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/tp53Flossies.py src/hg/makeDb/scripts/tp53/tp53Flossies.py
index 3410cf07bef..580695ca24b 100644
--- src/hg/makeDb/scripts/tp53/tp53Flossies.py
+++ src/hg/makeDb/scripts/tp53/tp53Flossies.py
@@ -132,31 +132,31 @@
 
 def hg19_to_hg38_lift(records, outdir):
     """Lift FLOSSIES hg19 coords to hg38; return dict keyed on variant_id."""
     chain = "/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz"
     if not os.path.exists(chain):
         chain = "/cluster/data/hg19/bed/liftOver/hg19ToHg38.over.chain.gz"
     in_bed = os.path.join(outdir, ".flossies_lift_in.bed")
     out_bed = os.path.join(outdir, ".flossies_lift_out.bed")
     unmapped = os.path.join(outdir, ".flossies_unmapped.bed")
     with open(in_bed, 'w') as f:
         for v in records:
             pos = int(v['pos'])
             ref = v['ref']
             f.write("chr{}\t{}\t{}\t{}\n".format(
                 v['chrom'], pos - 1, pos - 1 + len(ref), v['variant_id']))
-    lib.bash("liftOver {} {} {} {}".format(in_bed, chain, out_bed, unmapped))
+    lib.run_liftOver(in_bed, chain, out_bed, unmapped)
     lookup = {}
     with open(out_bed) as f:
         for line in f:
             flds = line.rstrip("\n").split("\t")
             if len(flds) >= 4:
                 lookup[flds[3]] = (flds[0], int(flds[1]), int(flds[2]))
     for p in [in_bed, out_bed, unmapped]:
         if os.path.exists(p):
             os.remove(p)
     return lookup
 
 
 def emit_rows(records, assembly, hg38_lookup):
     """Build BED9+8 lines for the requested assembly."""
     lines = []
@@ -220,31 +220,31 @@
         print("  liftOver matched {}/{} variants".format(
             len(hg38_lookup), len(records)))
         lines = emit_rows(records, 'hg38', hg38_lookup)
     else:
         lines = emit_rows(records, 'hg19', None)
     print("  {} BED rows".format(len(lines)))
 
     bs2_count = sum(1 for L in lines if "\tBS2\t" in L)
     print("  BS2 applicable: {}".format(bs2_count))
 
     as_file = os.path.join(outdir, "TP53Flossies.as")
     lib.write_autosql(as_file, AUTOSQL)
     bed = os.path.join(outdir, "TP53Flossies_{}.bed".format(db))
     with open(bed, 'w') as f:
         f.write("\n".join(lines) + "\n")
-    lib.bash("sort -k1,1 -k2,2n {0} -o {0}".format(bed))
+    lib.run_sort_bed(bed)
     bb = os.path.join(outdir, "TP53Flossies{}.bb".format(db.capitalize()))
     lib.run_bedToBigBed(bed, as_file, bb, lib.chrom_sizes_path(db), "bed9+10")
     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)