Feature#

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

new style annotation, created on demand

Attributes:

biotype
map
name
parent
reversed: whether Feature is on the reverse strand relative to bound object
seqid
xattr

Methods

`as_one_span`()	returns a feature that preserves any gaps
`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`()	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() → Self#: returns a feature that preserves any gaps

property biotype: str#

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

get_coordinates() → list[tuple[int, int]]#: 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#

property name: str#

property parent: Sequence | Alignment#

remapped_to(grandparent, gmap)#

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

property seqid: str#

shadow() → Self#: returns new instance corresponding to disjoint of self coordinates

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#