Codon export

from kallima import KallimaClient

client = KallimaClient(api_key)

strategies = client.codon_exports.strategies()
for s in strategies:
    print(s["name"], "—", s["description"])

batch = client.codon_exports.submit_batch(
    strategy="cai_max",
    host="cho",
    output_formats=["fasta", "genbank"],
    items=[
        {"variant_id": "var_aaa..."},
        {"variant_id": "var_bbb..."},
    ],
)

batch_id = batch["batch_id"]
job_ids = batch["job_ids"]    # one per variant, same order as items
export_ids = batch["export_ids"]  # one per variant

batch = client.codon_exports.submit_batch(
    strategy="cai_max",
    host="cho",
    output_formats=["fasta"],
    items=[{"variant_id": "var_aaa..."}],
    options={
        "restriction_sites": ["EcoRI", "BamHI", "NotI"],
        "gc_min": 0.42,
        "gc_max": 0.58,
        "check_splice_sites": True,
        "splice_score_threshold": 0.85,
    },
)

export = client.codon_exports.get(export_id)
for v in export["violations"]:
    if v["type"] == "splice_site":
        print(v["detail"])  # "Putative cryptic splice donor at position 312 (score 0.87). …"

import time

for job_id in job_ids:
    job = client.jobs.get(job_id)
    while job.status not in ("completed", "failed", "canceled"):
        time.sleep(10)
        job = client.jobs.get(job_id)
    print(job_id, job.status)

for export_id in export_ids:
    export = client.codon_exports.get(export_id)
    if export["variable_cds"] is None:
        continue  # still running

    fasta_bytes = client.codon_exports.download(export_id, format="fasta")
    with open(f"{export_id}.fasta", "wb") as f:
        f.write(fasta_bytes)

    genbank_zip = client.codon_exports.download(export_id, format="genbank")
    with open(f"{export_id}.zip", "wb") as f:
        f.write(genbank_zip)

export = client.codon_exports.get(export_id)

print(export["strategy"])              # "cai_max"
print(export["host"])                  # "cho"
print(export["constraints_satisfied"]) # bool — False if the optimizer hit hard constraints
print(export["violations"])            # list of unmet constraint descriptions
print(export["metrics"])               # dict — CAI, GC content, rare codon count, etc.

# Browse available signal peptides
for sp in client.codon_exports.signal_peptides():
    print(sp["id"], sp["name"])

# Attach per chain when submitting
batch = client.codon_exports.submit_batch(
    strategy="cai_max",
    host="cho",
    output_formats=["fasta"],
    items=[
        {
            "variant_id": "var_aaa...",
            "signal_peptides": {
                "H": "sp-uuid-for-heavy",
                "L": "sp-uuid-for-light",
            },
        }
    ],
)

import os, time
from kallima import KallimaClient

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

variant_ids = ["var_aaa...", "var_bbb..."]
items = [{"variant_id": vid} for vid in variant_ids]

batch = client.codon_exports.submit_batch(
    strategy="cai_max",
    host="cho",
    output_formats=["fasta", "csv"],
    items=items,
)

for job_id, export_id in zip(batch["job_ids"], batch["export_ids"]):
    job = client.jobs.get(job_id)
    while job.status not in ("completed", "failed", "canceled"):
        time.sleep(10)
        job = client.jobs.get(job_id)

    if job.status != "completed":
        print(f"{job_id} failed")
        continue

    data = client.codon_exports.download(export_id, format="fasta")
    with open(f"{export_id}.fasta", "wb") as f:
        f.write(data)
    print(f"Saved {export_id}.fasta")