INNER CODE UNIT · Python

convert

antigenomics/vdjtools · python/vdjtools/cli/__init__.py:251

def convert(
    input: Path = typer.Argument(..., help="Clonotype file in any supported format."),
    fmt: str = _FMT, out: Optional[Path] = _OUT,
) -> None:
    """Read any supported format and write the canonical AIRR-junction table.

    Auto-detects native vdjtools / AIRR / Parquet and the third-party exports (MiXcr, MiGec,
    MiTCR, immunoSEQ, IMGT/HighV-QUEST, Vidjil, RTCR, TRUST4, arda). Output is TSV, or Parquet
    when ``-o`` ends in ``.parquet`` / ``.pq`` — the typed, columnar, at-scale store.
    """
    from vdjtools.io.batch import read

    try:
        _write(read(input, fmt=fmt), out)
    except ValueError as e:                          # unknown fmt / unrecognised header
        _err(str(e))

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