core.alignment.Aligned

core.alignment.Aligned(data, moltype, name=None, annotation_db=None)

A single sequence in an alignment.

Notes

This is a wrapper around a AlignedDataView. This class performs any complementing needed. It can be cast directly to a string or numpy array, e.g. numpy.array(<aligned instance>) returns a numpy unsigned 8-bit integer array.

Attributes

Name	Description
annotation_db	the annotation database for the collection
gapped_seq	Returns Sequence object, including gaps.
seq	the ungapped sequence.

Methods

Name	Description
from_map_and_aligned_data_view	Creates an Aligned instance from an indel map and AlignedDataView.
from_map_and_seq	Creates an Aligned instance from an indel map and a Sequence.
gap_vector	Returns gap_vector of positions.
make_feature	returns a feature, not written into annotation_db
parent_coordinates	returns seqid, start, stop, strand on the parent sequence
replace_annotation_db	public interface to assigning the annotation_db

from_map_and_aligned_data_view

core.alignment.Aligned.from_map_and_aligned_data_view(indel_map, seq)

Creates an Aligned instance from an indel map and AlignedDataView.

from_map_and_seq

core.alignment.Aligned.from_map_and_seq(indel_map, seq)

Creates an Aligned instance from an indel map and a Sequence.

gap_vector

core.alignment.Aligned.gap_vector()

Returns gap_vector of positions.

make_feature

core.alignment.Aligned.make_feature(feature, alignment)

returns a feature, not written into annotation_db

parent_coordinates

core.alignment.Aligned.parent_coordinates(seq_coords=False, apply_offset=False)

returns seqid, start, stop, strand on the parent sequence

Parameters

Name	Type	Description	Default
seq_coords	bool	if True, the coordinates for the unaligned sequence	False
apply_offset	bool	if True and seq_coords, adds annotation offset from parent	False

replace_annotation_db

core.alignment.Aligned.replace_annotation_db(value, check=True)

public interface to assigning the annotation_db

Parameters

Name	Type	Description	Default
value	AnnotationDbABC | list[AnnotationDbABC] | None	the annotation db instance	required
check	bool	whether to check value supports the feature interface	True

Notes

The check can be very expensive, so if you’re confident set it to False