INNER CODE UNIT · Python
models
antigenomics/vdjtools · python/vdjtools/cli/__init__.py:146
def models() -> None:
"""List the precomputed recombination models shipped with the package."""
from vdjtools.model import list_bundled
for src, loci in list_bundled().items():
typer.echo(f"{src:8s} {' '.join(loci) if loci else '(none)'}")
@app.command()
def pgen(
input: Path = typer.Argument(..., help="Table (TSV) or list of CDR3 sequences."),
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."),
column: Optional[str] = typer.Option(None, "--column", "-c", help="Sequence column (default: auto-detect / first)."),
v_col: Optional[str] = typer.Option(None, "--v-col", help="V-allele column to condition on (default: marginalize)."),
j_col: Optional[str] = typer.Option(None, "--j-col", help="J-allele column to condition on (default: marginalize)."),
seq_type: str = typer.Option("auto", "--type", help="auto | aa | nt."),