6577d5ee1319bbea85988c1c89179436b4a94edf
lrnassar
  Tue Jul 14 11:27:59 2026 -0700
Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446

- cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously
hardcoded the working directory for both its input TSV and its output (unlike
the 11 sibling scripts, and contrary to the makedoc's documented interface);
the build loop's flags were silently ignored. Output is unchanged (31,236
variants per assembly).
- Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr
diagnostics, comments, and docstrings across all scripts so build logs read
cleanly. The mouseOver / bigBed display strings intentionally keep their
entities.
- cmpVCEPWalsh2019.py: fix the stale docstring that described the
ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf
fallback, item L) and drop the unverified "163 rows" count.

Per code-review feedback on commit aa5669fe64. No track data changed.

diff --git src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
index ff57aa546b2..b5c5f5a5a5c 100644
--- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
+++ src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python3
 """
-Phase 1 &#8212; hgVai annotation layer for the Cardiomyopathy VCEP hub (RM37446).
+Phase 1 - hgVai annotation layer for the Cardiomyopathy VCEP hub (RM37446).
 
 Annotates the gnomAD-observed variant universe (the SAME universe used by the
 AF + Provisional tracks) with protein consequence via the internal UCSC tool
 hgVai (vai.pl), on the single MANE Select transcript per gene (ncbiRefSeqSelect).
 Reuses cmpVCEPAFfrequencies.fetch_gene_variants so the universe is identical.
 
 Output (consumed by Phase 2 cmpVCEPProvisionalClass):
   cmpVCEPAnnotate/cmpVCEPAnnotations.hg38.tsv   one row per (chrom,pos,ref,alt)
   cmpVCEPAnnotate/phase1_unmapped.tsv           universe variants with no VEP line
   cmpVCEPAnnotate/<gene>.vcf / <gene>.vep        per-gene intermediates
 
 Annotation is computed on hg38 only; Phase 2 codes carry to hg19 via the existing
 liftOver of the universe (annotation is transcript-based, assembly-independent).
 
 Usage:
@@ -68,31 +68,31 @@
 
 def parse_extra(extra):
     """Pull HGVSP and EXON out of the VEP Extra column (key=value;key=value)."""
     hgvsp, exon_n, exon_total = '', '', ''
     for kv in extra.split(';'):
         if kv.startswith('HGVSP='):
             hgvsp = kv[len('HGVSP='):]
         elif kv.startswith('EXON='):
             m = re.match(r'(\d+)/(\d+)', kv[len('EXON='):])
             if m:
                 exon_n, exon_total = m.group(1), m.group(2)
     return hgvsp, exon_n, exon_total
 
 
 def parse_vep(vep_path, gene):
-    """Parse one gene's VEP output &#8594; dict key (chrom,pos,ref,alt) &#8594; annotation.
+    """Parse one gene's VEP output -> dict key (chrom,pos,ref,alt) -> annotation.
     Aggregates SO terms across lines; keeps the coding fields from the line(s)
     that carry them."""
     ann = {}
     for line in open(vep_path):
         if line.startswith('#') or line.startswith('Uploaded'):
             continue
         f = line.rstrip('\n').split('\t')
         if len(f) < 14:
             continue
         parts = f[0].split(':')
         if len(parts) != 4:
             continue
         chrom, pos, ref, alt = parts[0], int(parts[1]), parts[2], parts[3]
         key = (chrom, pos, ref, alt)
         so = f[6]
@@ -153,37 +153,37 @@
         all_ann.update(ann)
         print(f'    {gene} ({mane["chrom"]} {mane["strand"]}): '
               f'{len(universe_keys)} universe, {len(ann)} annotated, '
               f'{sum(1 for k in universe_keys if k not in ann_keys)} unmapped')
 
     tsv = os.path.join(work, 'cmpVCEPAnnotations.hg38.tsv')
     with open(tsv, 'w') as fh:
         fh.write('#chrom\tpos\tref\talt\tgene\tsoTerms\tproteinPos\taaRef\taaAlt\t'
                  'codonChange\texonNum\texonTotal\thgvsp\tcdnaPos\n')
         for (chrom, pos, ref, alt), r in sorted(all_ann.items(), key=lambda x: (x[0][0], x[0][1])):
             fh.write('\t'.join([
                 chrom, str(pos), ref, alt, r['gene'],
                 ','.join(sorted(r['so'])), r['proteinPos'], r['aaRef'], r['aaAlt'],
                 r['codon'], r['exonNum'], r['exonTotal'], r['hgvsp'], r['cdnaPos'],
             ]) + '\n')
-    print(f'  wrote {len(all_ann)} annotations &#8594; {tsv}')
+    print(f'  wrote {len(all_ann)} annotations -> {tsv}')
 
     unmapped_path = os.path.join(work, 'phase1_unmapped.tsv')
     with open(unmapped_path, 'w') as fh:
         fh.write('#gene\tchrom\tpos\tref\talt\n')
         for row in unmapped:
             fh.write('\t'.join(str(x) for x in row) + '\n')
-    print(f'  {len(unmapped)} unmapped universe variants logged &#8594; {unmapped_path}')
+    print(f'  {len(unmapped)} unmapped universe variants logged -> {unmapped_path}')
 
     # SO-term summary for sanity
     from collections import Counter
     so_counter = Counter()
     for r in all_ann.values():
         for s in r['so']:
             so_counter[s] += 1
     print('  SO-term distribution:')
     for s, c in so_counter.most_common():
         print(f'    {c:6d}  {s}')
 
 
 if __name__ == '__main__':
     main()