Immunogenicity analysis

from kallima import KallimaClient

client = KallimaClient(api_key)

job = client.immunogenicity_analyses.submit(variant_id=variant_id)
job.wait(timeout=300)

result = job.results

print(result["risk_score"])   # composite immunogenicity risk, 0–1
print(result["mhc1_risk"])    # MHC class I risk, 0–1
print(result["mhc2_risk"])    # MHC class II risk, 0–1
print(result["bcell_risk"])   # linear B-cell epitope risk, 0–1

for epitope in result["mhc1_epitopes"] or []:
    print(epitope["peptide"], epitope["allele"], epitope["affinity_nm"])

for epitope in result["mhc2_epitopes"] or []:
    print(epitope["peptide"], epitope["allele"], epitope["score"])

for epitope in result["bcell_epitopes"] or []:
    print(epitope["start"], epitope["end"], epitope["sequence"])

for suggestion in result["deimmunization_suggestions"] or []:
    print(suggestion["position"], suggestion["wild_type"], suggestion["mutation"],
          suggestion["mhc1_risk_delta"], suggestion["mhc2_risk_delta"])

print(result["model_versions"])  # e.g. {"mhcflurry": "2.1.4"}

import os
from kallima import KallimaClient

client = KallimaClient(os.environ["KALLIMA_API_KEY"])

variant_ids = ["var_aaa...", "var_bbb...", "var_ccc..."]
jobs = [client.immunogenicity_analyses.submit(vid) for vid in variant_ids]

for job in jobs:
    job.wait(timeout=300)
    r = job.results
    print(f"{job.variant_id}  MHC-II risk: {r['mhc2_risk']:.2f}  B-cell: {r['bcell_risk']:.2f}")

for job in client.immunogenicity_analyses.list(variant_id=variant_id):
    print(job.id, job.status, job["created_at"])