core.annotation.Feature

core.annotation.Feature(parent, seqid, map, biotype, name, strand, xattr=None)

new style annotation, created on demand

Attributes

Name	Description
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

Name	Description
as_one_span	returns a feature that preserves any gaps in the underlying sequence
get_children	generator returns sub-features of self optionally matching biotype
get_coordinates	returns sequence coordinates of this Feature as
get_drawable	returns plotly trace
get_parent	generator returns parent features of self optionally matching biotype
get_slice	The corresponding sequence fragment.
shadow	returns new instance corresponding to disjoint of self coordinates
to_dict	returns
union	return as a single Feature
without_lost_spans	Keeps only the parts which are actually present in the underlying sequence

core.annotation.Feature.as_one_span(name=None)

returns a feature that preserves any gaps in the underlying sequence

Name	Type	Description	Default
name	str \| None	The name of the one-span feature, by default ‘one-span ’	`None`

core.annotation.Feature.get_children(biotype=None, **kwargs)

generator returns sub-features of self optionally matching biotype

core.annotation.Feature.get_coordinates()

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

core.annotation.Feature.get_drawable()

returns plotly trace

core.annotation.Feature.get_parent(**kwargs)

generator returns parent features of self optionally matching biotype

core.annotation.Feature.get_slice(
    complete=False,
    allow_gaps=False,
    apply_name=True,
)

The corresponding sequence fragment.

Name	Type	Description	Default
complete	bool	if feature not complete on parent, causes an exception to be raised. If False, gaps are removed.	`False`
allow_gaps	bool	if on an alignment, includes the gap positions	`False`
apply_name	bool	assigns self.name to the resulting seq.name	`True`

Name	Type	Description
	a slice of self.parent

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

core.annotation.Feature.shadow(name=None)

returns new instance corresponding to disjoint of self coordinates

Name	Type	Description	Default
name	str \| None	The name of the shadow feature, by default ‘not ’	`None`

core.annotation.Feature.to_dict()

returns

core.annotation.Feature.union(features)

return as a single Feature

Overlapping spans are merged

core.annotation.Feature.without_lost_spans()

Keeps only the parts which are actually present in the underlying sequence