cogent3.core.seq_storage.SeqsData#

class SeqsData(*, data: Mapping[str, str | bytes | NumpyIntArrayType], alphabet: c3_alphabet.CharAlphabet[Any], 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_hash`(seqid)	returns hash of seqid
`get_seq_bytes`(*, seqid[, start, stop, step])	Return ungapped sequence corresponding to seqid as a bytes string.
`get_seq_length`(seqid)	return length for seqid
`get_seq_str`(*, seqid[, start, stop, step])	Return ungapped sequence corresponding to seqid as a string.
`get_view`(seqid)	reurns view of sequence data for seqid

from_seqs
get_seq_array
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.