skills/bioskills/bio-tcr-bcr-analysis-specificity-annotation/scripts/specificity_annotation.py

• synthetic_repertoire · function · L13-L18 — def synthetic_repertoire()
• synthetic_vdjdb · function · L21-L28 — def synthetic_vdjdb(): # A curated-style export: CDR3 + V + restricting HLA + epitope + confidence score 0-3.
• annotate_by_db · function · L31-L38 — def annotate_by_db(repertoire, vdjdb, donor_hla, min_confidence=1): # vdjdb_score 0-3: 0 = critical info missing, 3 = independently validated; >=1 drops single-observation noise.
• beta_neighborhoods · function · L41-L46 — def beta_neighborhoods(clone_df, radius=50): # radius in TCRdist units; ~50 is a common meta-clonotype inclusion radius (Mayer-Blackwell 2021 eLife 10:e68605).
• load_beta_pgen_model · function · L49-L59 — def load_beta_pgen_model(model_dir)
• main · function · L62-L88 — def main()