SeqView#

class SeqView(*, parent: str | bytes | ndarray[tuple[Any, ...], dtype[integer]], alphabet: CharAlphabet[Any], parent_len: int, seqid: str | None = None, slice_record: SliceRecordABC | None = None, offset: int = 0)#

Provides a view of a sequence with support for slicing operations.

This class represents a view of a sequence. It uses SliceRecord to enable efficient slicing without altering the original sequence data.

Parameters:

parent: the original sequence data
alphabet: the alphabet object defining valid characters for the sequence
seqid: the name or identifier of the sequence
parent_len: the length of the sequence. Defaults to the length of the input sequence

Attributes:

alphabet
array_value: returns the sequence as a array of indices
bytes_value: returns the sequence as a bytes string
is_reversed: whether the sequence is reversed
offset: the annotation offset of this view
parent
parent_len: length of the parent sequence
parent_offset: returns the offset from the true parent
seqid: name of the sequence
slice_record: the slice state of this view
str_value: returns the sequence as a string

Methods

`copy`([sliced])	returns copy
`parent_coords`(*[, apply_offset])	returns coordinates on parent
`with_offset`(offset)	returns new instance with annotation offset set

Notes

It utilises the alphabet object to allow providing different types such as strings or numpy arrays, corresponding to its underlying data.

alphabet#

property array_value: ndarray[tuple[Any, ...], dtype[integer]]#: returns the sequence as a array of indices

property bytes_value: bytes#: returns the sequence as a bytes string

copy(sliced: bool = False) → Self#

returns copy

Parameters:

sliced: if True, the underlying sequence is truncated and the start/stop adjusted

property is_reversed: bool#: whether the sequence is reversed

property offset: int#: the annotation offset of this view

parent#

parent_coords(*, apply_offset: bool = False, **kwargs) → tuple[str, int, int, int]#

returns coordinates on parent

Parameters:

apply_offset: if True adds annotation offset from parent

Returns:

parent seqid, start, stop, strand

property parent_len: int#: length of the parent sequence

property parent_offset: int#

returns the offset from the true parent

Notes

If from storage with an offset attribute, returns that value or 0

property seqid: str | None#: name of the sequence

property slice_record: SliceRecordABC#: the slice state of this view

property str_value: str#: returns the sequence as a string

with_offset(offset: int) → Self#: returns new instance with annotation offset set