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/tp53CancerHotspots.py src/hg/makeDb/scripts/tp53/tp53CancerHotspots.py index 09901e7a9f4..202633ed040 100644 --- src/hg/makeDb/scripts/tp53/tp53CancerHotspots.py +++ src/hg/makeDb/scripts/tp53/tp53CancerHotspots.py @@ -1,179 +1,179 @@ #!/usr/bin/env python3 """ TP53 VCEP cancerhotspots.org subtrack generator (PM1 Evidence composite). Fetches cancerhotspots.org single-residue hotspots, filters to TP53, and emits a per-AA-change bigBed 9+4 with ACMG PM1 strength assignment: PM1_Moderate (+2 pts) >=10 somatic occurrences of this exact aa change PM1_Supporting (+1 pt) 2-9 occurrences Synonymous (WT->WT) and stop-gain (*) variants are excluded; only missense. Live pull with a cached-snapshot fallback. """ import argparse import json import os import sys import urllib.request sys.path.insert(0, os.path.dirname(os.path.abspath(__file__))) import tp53FuncLib as lib DEFAULT_OUTDIR = "/hive/users/lrnassar/claude/RM37399/cancerHotspots" SNAPSHOT_NAME = "cancerhotspots_single.json" API_URL = "https://www.cancerhotspots.org/api/hotspots/single" COLOR_MOD = "230,3,131" # fuchsia — PM1_Moderate COLOR_SUP = "245,182,207" # light fuchsia — PM1_Supporting AUTOSQL = """table TP53CancerHotspots "TP53 somatic hotspots from cancerhotspots.org mapped to ACMG PM1 strength" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Amino acid change (e.g. R175H)" uint score; "Not used, all 0" char[1] strand; "Not used, all ." uint thickStart; "Same as chromStart" uint thickEnd; "Same as chromEnd" uint reserved; "RGB color" string acmgCode; "PM1_Moderate or PM1_Supporting" string points; "Tavtigian points contribution" uint somaticCount; "Somatic occurrence count (cancerhotspots.org)" lstring _mouseOver; "HTML mouseover" ) """ def fetch_or_load(outdir): path = os.path.join(outdir, SNAPSHOT_NAME) try: req = urllib.request.Request(API_URL, headers={'User-Agent': 'UCSC-kent/TP53-hub'}) with urllib.request.urlopen(req, timeout=30) as resp: body = resp.read() data = json.loads(body) # Write snapshot on success with open(path, 'wb') as f: f.write(body) print(" fetched {} records from cancerhotspots.org".format(len(data))) return data except Exception as e: if os.path.exists(path): print(" WARNING: live fetch failed ({}); falling back to snapshot {}".format(e, path)) with open(path) as f: return json.load(f) raise RuntimeError("cancerhotspots fetch failed and no snapshot: {}".format(e)) def records_for_tp53(data): out = [] for h in data: if h.get('hugoSymbol') != 'TP53': continue res = h.get('residue', '') if not res: continue # residue is like "R175"; first char = WT aa, rest = codon position. # cancerhotspots.org also reports splice-site somatic hotspots where # residue starts with 'X' and variants contain 'sp'. Those are NOT # missense and must not be classified PM1 (CSpec §PM1 is missense only). wt = res[0] if wt == 'X' or not wt.isalpha(): continue try: codon = int(res[1:]) except ValueError: continue variants = h.get('variantAminoAcid') or {} for alt, count in variants.items(): if alt == wt: # synonymous — not missense continue if alt in ('*', 'X'): # stop-gain — handled by PVS1, not PM1 continue if not alt.isalpha() or len(alt) != 1: # splice-site codes ("sp", "fs", etc.) are not missense continue if count is None or count < 2: continue if count >= 10: acmg, points, color = "PM1_Moderate", "+2", COLOR_MOD else: acmg, points, color = "PM1_Supporting", "+1", COLOR_SUP out.append({ 'wt': wt, 'codon': codon, 'alt': alt, 'count': count, 'acmg': acmg, 'points': points, 'color': color, 'name': "{}{}{}".format(wt, codon, alt), }) return out def mouseover(rec): return ( "<b>{acmg}</b> ({points} pts)" "<br><b>Variant:</b> {name} (TP53 NP_000537.3)" "<br><b>Somatic occurrences (cancerhotspots.org):</b> {count}" "<br><b>Codon:</b> {codon}" "<br><b>Source:</b> cancerhotspots.org — PM1 per CSpec GN009 v2.4.0" ).format(**rec) def generate_bed(records, tx): lines = [] chrom = tx['chrom'] for rec in records: segs = lib.aa_codon_genomic(rec['codon'], tx) if not segs: continue for g_start, g_end, _ex in segs: lines.append("\t".join([ chrom, str(g_start), str(g_end), rec['name'], "0", ".", str(g_start), str(g_end), rec['color'], rec['acmg'], rec['points'], str(rec['count']), mouseover(rec), ])) return lines def build(db, outdir): print("=== {} ===".format(db)) os.makedirs(outdir, exist_ok=True) data = fetch_or_load(outdir) records = records_for_tp53(data) print(" {} TP53 PM1 records".format(len(records))) tx = lib.get_transcript_info(db) bed_lines = generate_bed(records, tx) print(" {} BED rows".format(len(bed_lines))) as_file = os.path.join(outdir, "TP53CancerHotspots.as") lib.write_autosql(as_file, AUTOSQL) bed = os.path.join(outdir, "TP53CancerHotspots_{}.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, "TP53CancerHotspots{}.bb".format(db.capitalize())) lib.run_bedToBigBed(bed, as_file, bb, lib.chrom_sizes_path(db), "bed9+4") 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.') args = p.parse_args() dbs = args.db if args.db else ['hg38'] for db in dbs: build(db, args.output_dir) if __name__ == "__main__": main()