AlignedDataView#

class AlignedDataView(*, parent: AlignedSeqsDataABC, seqid: str, alphabet: AlphabetABC, slice_record: SliceRecord | None = None)#

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

Attributes:

alphabet
array_value: returns the numpy array of indices for the ungapped sequence
bytes_value: returns the bytes value of the ungapped sequence
gapped_array_value: returns the numpy array of indices for the gapped sequence
gapped_bytes_value: returns the bytes value of the gapped sequence
gapped_str_value: returns the string value of the gapped sequence
is_reversed: whether the sliced view is reversed relative to the parent
map: indel map (gaps) for the sequence
offset: the slice offset of this view
parent
parent_len: length of the parent sequence
parent_offset: returns the offset from the true parent
seqid: the name of the sequence
slice_record: the slice record for this view
str_value: returns the string value of the ungapped sequence

Methods

`copy`([sliced])	just returns self
`get_seq_view`()	returns view of ungapped sequence data for seqid
`parent_coords`(*[, seq_coords, apply_offset])	returns seqid, start, stop, strand on the parent
`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 Aligned object which has a moltype. The slice_record attribute is shared with the containing Alignment.

alphabet#

property array_value: ndarray#: returns the numpy array of indices for the ungapped sequence

property bytes_value: bytes#: returns the bytes value of the ungapped sequence

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

property gapped_array_value: ndarray#: returns the numpy array of indices for the gapped sequence

property gapped_bytes_value: bytes#: returns the bytes value of the gapped sequence

property gapped_str_value: str#: returns the string value of the gapped sequence

get_seq_view() → SeqViewABC#: returns view of ungapped sequence data for seqid

property is_reversed: bool#: whether the sliced view is reversed relative to the parent

property map: IndelMap#: indel map (gaps) for the sequence

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

parent#

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

returns seqid, start, stop, strand on the parent

Parameters:

seq_coords: if True, parent is the ungapped sequence
apply_offset: if True and seq_coords, adds annotation offset from parent

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#: the name of the sequence

property slice_record: SliceRecordABC#: the slice record for this view

property str_value: str#: returns the string value of the ungapped sequence

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