Feature#

class Feature(*, parent: Sequence | Alignment, seqid: str, map: FeatureMap, biotype: str, name: str, strand: int | str, xattr: dict[str, Any] | None = None)#

new style annotation, created on demand

Attributes:

biotype: type of biological feature
map: coordinate map and properties of this feature
name: name of the feature
parent: sequence or aligned or alignment
reversed: whether Feature is on the reverse strand relative to bound object
seqid: the sequence id of the parent sequence
xattr: extra attributes for this feature

Methods

`as_one_span`([name])	returns a feature that preserves any gaps in the underlying sequence
`get_children`([biotype])	generator returns sub-features of self optionally matching biotype
`get_coordinates`()	returns sequence coordinates of this Feature as [(start1, end1), ...]
`get_drawable`()	returns plotly trace
`get_parent`(**kwargs)	generator returns parent features of self optionally matching biotype
`get_slice`([complete, allow_gaps, apply_name])	The corresponding sequence fragment.
`shadow`([name])	returns new instance corresponding to disjoint of self coordinates
`to_dict`()	returns
`union`(features)	return as a single Feature
`without_lost_spans`()	Keeps only the parts which are actually present in the underlying sequence

remapped_to

as_one_span(name: str | None = None) → Self#

returns a feature that preserves any gaps in the underlying sequence

Parameters:

name: The name of the one-span feature, by default ‘one-span <self name>’

property biotype: str#: type of biological feature

get_children(biotype: str | None = None, **kwargs) → Iterable[Self]#: generator returns sub-features of self optionally matching biotype

get_coordinates() → Sequence[Sequence[int | int32 | int64]]#: returns sequence coordinates of this Feature as [(start1, end1), …]

get_drawable() → Shape#: returns plotly trace

get_parent(**kwargs) → Iterable[Self]#: generator returns parent features of self optionally matching biotype

get_slice(complete: bool = False, allow_gaps: bool = False, apply_name: bool = True) → Sequence | Alignment#

The corresponding sequence fragment.

Parameters:

complete: if feature not complete on parent, causes an exception to be raised. If False, gaps are removed.
allow_gaps: if on an alignment, includes the gap positions
apply_name: assigns self.name to the resulting seq.name

Returns:

a slice of self.parent

Notes

If ‘complete’ is true and the full length of this feature is not present in the sequence, then this method will fail.

property map: FeatureMap#: coordinate map and properties of this feature

property name: str#: name of the feature

property parent: Sequence | Alignment#: sequence or aligned or alignment

remapped_to(grandparent, gmap) → Self#

property reversed: bool#: whether Feature is on the reverse strand relative to bound object

property seqid: str#: the sequence id of the parent sequence

shadow(name: str | None = None) → Self#

returns new instance corresponding to disjoint of self coordinates

Parameters:

name: The name of the shadow feature, by default ‘not <self name>’

to_dict() → dict[str, Any]#: returns

union(features: Iterable) → Self#

return as a single Feature

Notes

Overlapping spans are merged

without_lost_spans() → Self#: Keeps only the parts which are actually present in the underlying sequence

property xattr: dict[str, Any] | None#: extra attributes for this feature