SeqsData#

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

The builtin cogent3 implementation of sequence storage 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: the character alphabet for validating, encoding, decoding sequences
names: returns the names of the sequences in the storage
offset: annotation offsets for each sequence
reversed_seqs: names of sequences that are reverse complemented

Methods

`add_seqs`(seqs[, force_unique_keys, offset])	Returns a new SeqsData object with added sequences.
`copy`(**kwargs)	shallow copy of self
`get_seq_length`(seqid)	return length for seqid
`get_view`(seqid)	reurns view of sequence data for seqid

from_seqs
get_seq_array
get_seq_bytes
get_seq_str
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: bool = True, offset: dict[str, int] | None = 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: CharAlphabet#: the character alphabet for validating, encoding, decoding sequences

copy(**kwargs) → Self#

shallow copy of self

Notes

kwargs are passed to constructor and will over-ride existing values

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#: reurns view of sequence data for seqid

property names: tuple[str, ...]#: returns the names of the sequences in the storage

property offset: dict[str, int]#: annotation offsets for each sequence

property reversed_seqs: frozenset[str]#: names of sequences that are reverse complemented

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