INNER CODE UNIT · Python
filter_
antigenomics/vdjtools · python/vdjtools/cli/__init__.py:285
def filter_(
input: Path = typer.Argument(..., help="Clonotype sample file."),
fmt: str = _FMT, out: Optional[Path] = _OUT,
productive: bool = typer.Option(False, "--productive", help="Keep only AIRR-productive rearrangements (in-frame, stop-free)."),
nonproductive: bool = typer.Option(False, "--nonproductive", help="Keep only NON-productive rearrangements (the complement)."),
functional_genes: bool = typer.Option(False, "--functional-genes", help="Keep only rearrangements whose V/J are IMGT-functional (F). A DIFFERENT axis from --productive."),
keep_orf: bool = typer.Option(False, "--keep-orf", help="With --functional-genes: keep IMGT ORF alleles as well as F."),
recompute_frequencies: bool = typer.Option(True, "--recompute-frequencies/--keep-frequencies", help="Renormalise `frequency` over the survivors (default), or leave the file's own frequencies untouched."),
coding: bool = typer.Option(False, "--coding", hidden=True, help="Deprecated alias for --productive."),
noncoding: bool = typer.Option(False, "--noncoding", hidden=True, help="Deprecated alias for --nonproductive."),
min_len: Optional[int] = typer.Option(None, "--min-len", help="Shortest junction_aa to keep, INCLUSIVE (default bound 5)."),
max_len: Optional[int] = typer.Option(None, "--max-len", help="Longest junction_aa to keep, INCLUSIVE (default bound 60)."),
min_freq: Optional[float] = typer.Option(None, "--min-freq", help="Keep clonotypes with frequency >= this."),
v: Optional[str] = typer.Option(None, "--v", help="Comma-separated V segments (prefix ok)."),
j: Optional[str] = typer.Option(None, "--j", help="Comma-separated J segments (prefix ok)."),
remove: bool = typer.Option(False, "--remove", help="With --v/--j: remove the listed segments instead of keeping them."),
) -> None:
"""Filter clonotypes: productive / non-productive, IMGT-functional genes, frequency, V/J segment.