Feature#

class Feature(*, parent, seqid: str, map: FeatureMap, biotype: str, name: str, strand: str)#

new style annotation, created on demand

Attributes:

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

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])	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

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

get_coordinates()#: returns sequence coordinates of this Feature as [(start1, end1), …]

get_parent(**kwargs)#: generator returns parent features of self optionally matching biotype

get_slice(complete: bool = False, allow_gaps: bool = False)#

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

Returns:

Notes

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

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

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

union(features: Iterable)#

return as a single Feature

Notes

Overlapping spans are merged

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