"""``uchrom.tl`` — flat, scanpy-style aliases for analysis *tools*.
Tools add annotations (structures, features, embeddings) to a
``ChromData``. The implementations live in the domain modules
(``uchrom.strc``, ``uchrom.fea``, …); these aliases only dispatch on
``method=`` and forward every other keyword unchanged, so they follow the
same calling convention (``chrom=None``, ``params=``, ``key_added=``,
``copy=``)::
import uchrom as uc
uc.tl.call_tads(cd, method="arcfish") # strc.tad.call_tads_by_pval
uc.tl.call_loops(cd) # strc.loop.call_loops_axiswise_f
uc.tl.call_compartments(cd) # strc.comp.call_compartments_axes_pc
uc.tl.reconstruct_sc("cell.pairs") # recon.sc.reconstruct_ember (EMber)
"""
from __future__ import annotations
from typing import Callable, Dict
def _tad_methods() -> Dict[str, Callable]:
from uchrom.strc.tad import call_domains_fishnet, call_tads_by_pval, call_tads_di
return {
"arcfish": call_tads_by_pval,
"pval": call_tads_by_pval,
"fishnet": call_domains_fishnet,
"di": call_tads_di,
}
def _dispatch(kind: str, methods: Dict[str, Callable], method: str):
try:
return methods[method]
except KeyError:
raise ValueError(f"unknown {kind} method {method!r}; choose from {sorted(methods)}") from None
[docs]
def call_tads(cd, *, method: str = "arcfish", **kwargs):
"""Call TADs / domains.
``method``: ``"arcfish"`` (alias ``"pval"``) →
:func:`uchrom.strc.tad.call_tads_by_pval`; ``"fishnet"`` →
:func:`uchrom.strc.tad.call_domains_fishnet`; ``"di"`` →
:func:`uchrom.strc.tad.call_tads_di` (linked Hi-C contacts).
"""
return _dispatch("TAD", _tad_methods(), method)(cd, **kwargs)
[docs]
def call_loops(cd, *, method: str = "axiswise_f", **kwargs):
"""Call loops. ``method``: ``"axiswise_f"`` →
:func:`uchrom.strc.loop.call_loops_axiswise_f`."""
from uchrom.strc.loop import call_loops_axiswise_f
return _dispatch("loop", {"axiswise_f": call_loops_axiswise_f}, method)(cd, **kwargs)
[docs]
def call_compartments(cd, *, method: str = "axes_pc", **kwargs):
"""Call A/B compartments. ``method``: ``"axes_pc"`` →
:func:`uchrom.strc.comp.call_compartments_axes_pc`."""
from uchrom.strc.comp import call_compartments_axes_pc
return _dispatch("compartment", {"axes_pc": call_compartments_axes_pc}, method)(cd, **kwargs)
[docs]
def reconstruct_sc(contacts, *, method: str = "ember", **kwargs):
"""Single-cell Hi-C 3-D reconstruction -> new ``ChromData``. ``method``:
``"ember"`` -> :func:`uchrom.recon.sc.reconstruct_ember`; ``"nucdyn"`` ->
:func:`uchrom.recon.sc.reconstruct_nucdyn`."""
from uchrom.recon.sc import reconstruct_ember, reconstruct_nucdyn
return _dispatch("single-cell reconstruction", {"ember": reconstruct_ember, "nucdyn": reconstruct_nucdyn}, method)(
contacts, **kwargs)
__all__ = ["call_compartments", "call_loops", "call_tads", "reconstruct_sc"]