INNER CODE UNIT · Python
generate
antigenomics/vdjtools · python/vdjtools/cli/__init__.py:204
def generate(
model: Optional[str] = typer.Option(None, "--model", "-m", help="Built-in locus: TRA TRB TRG TRD IGH IGK IGL."),
source: str = typer.Option("olga", help="Built-in model set: olga | learned."),
model_path: Optional[Path] = typer.Option(None, help="Load a custom model directory instead of a built-in."),
n: int = typer.Option(100, "--number", "-n", help="Number of sequences to generate."),
seed: Optional[int] = typer.Option(None, help="Random seed for reproducible draws."),
productive: bool = typer.Option(False, help="Only keep in-frame, stop-free (productive) rearrangements."),
out: Optional[Path] = typer.Option(None, "--out", "-o", help="Output TSV (default: stdout)."),
) -> None:
"""Sample recombined sequences from a model — like ``olga-generate_sequences``.
Emits ``junction_nt, junction_aa, v_call, d_call, d2_call, j_call, productive`` (``d2_call`` is the
tandem D on the learned D-bearing loci; null otherwise).
"""
from vdjtools.model.generate import generate as _generate
m = _load_model(model, source, model_path)
_write(_generate(m, n, seed=seed, productive_only=productive), out)