SeqsData

class SeqsData(*, data: dict[str, str | bytes | ndarray[int]], alphabet: AlphabetABC, offset: dict[str, int] = None, check: bool = True)

The builtin cogent3 implementation of a collection of sequences underlying a SequenceCollection. The sequence data is stored as numpy arrays. Indexing this object (using an int or seq name) returns a SeqDataView, which can realise the corresponding slice as a string, bytes, or numpy array via the alphabet.

Attributes:

alphabet

names

offset

Methods

add_seqs(seqs[, force_unique_keys, offset])	Returns a new SeqsData object with added sequences.
get_seq_length(seqid)	return length for seqid

from_seqs
get_seq_array
get_seq_bytes
get_seq_str
get_view
to_alphabet

Notes

Methods on this object only accepts plust strand start, stop and step indices for selecting segments of data. It can return the gap coordinates for a sequence as used by IndelMap.

add_seqs(seqs: dict[str, str | bytes | ndarray[int]], force_unique_keys=True, offset=None) → SeqsData

Returns a new SeqsData object with added sequences. If force_unique_keys is True, raises ValueError if any names already exist in the collection.

property alphabet: AlphabetABC

classmethod from_seqs(*, data: dict[str, str | bytes | ndarray[int]], alphabet: AlphabetABC, **kwargs)

get_seq_array(*, seqid: str, start: int | None = None, stop: int | None = None, step: int | None = None) → ndarray

get_seq_bytes(*, seqid: str, start: int | None = None, stop: int | None = None, step: int | None = None) → bytes

get_seq_length(seqid: str) → int

return length for seqid

get_seq_str(*, seqid: str, start: int | None = None, stop: int | None = None, step: int | None = None) → str

get_view(seqid: str) → SeqDataView

property names: list

property offset: dict[str, int]

to_alphabet(alphabet: AlphabetABC, check_valid=True) → SeqsData