SeqDataView#

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

A view class for SeqsData, providing methods for different representations of a single sequence.

Attributes:

alphabet
array_value: returns the sequence as a numpy array
bytes_value: returns the sequence as bytes
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
`to_rich_dict`()	returns a json serialisable dict.
`with_offset`(offset)	returns new instance with annotation offset set

Notes

str_value / array_value are not complemented, but can be reversed. The latter is done by the Sequence object which has a moltype.

alphabet#

property array_value: ndarray#: returns the sequence as a numpy array

property bytes_value: bytes#: returns the sequence as bytes

copy(sliced: bool = False) → Self#: returns copy

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

to_rich_dict() → dict[str, str | dict[str, str]]#

returns a json serialisable dict.

Warning

This method is not intended to provide serialisation of this object, instead, it is intended for usage by an enclosing class.

Notes

This method will slice the underlying sequence to the start and stop values

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