core.seq_storage.SeqsData
core.seq_storage.SeqsData(
data,
alphabet,
offset=None,
check=True,
reversed_seqs=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.
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.
Attributes
| Name | Description |
|---|---|
| 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
| Name | Description |
|---|---|
| add_seqs | Returns a new SeqsData object with added sequences. If force_unique_keys |
| copy | shallow copy of self |
| get_hash | returns hash of seqid |
| get_seq_bytes | Return ungapped sequence corresponding to seqid as a bytes string. |
| get_seq_length | return length for seqid |
| get_seq_str | Return ungapped sequence corresponding to seqid as a string. |
| get_view | reurns view of sequence data for seqid |
add_seqs
core.seq_storage.SeqsData.add_seqs(seqs, force_unique_keys=True, offset=None)Returns a new SeqsData object with added sequences. If force_unique_keys is True, raises ValueError if any names already exist in the collection.
copy
core.seq_storage.SeqsData.copy(**kwargs)shallow copy of self
Notes
kwargs are passed to constructor and will over-ride existing values
get_hash
core.seq_storage.SeqsData.get_hash(seqid)returns hash of seqid
get_seq_bytes
core.seq_storage.SeqsData.get_seq_bytes(seqid, start=None, stop=None, step=None)Return ungapped sequence corresponding to seqid as a bytes string. start/stop are in sequence coordinates. Excludes gaps.
get_seq_length
core.seq_storage.SeqsData.get_seq_length(seqid)return length for seqid
get_seq_str
core.seq_storage.SeqsData.get_seq_str(seqid, start=None, stop=None, step=None)Return ungapped sequence corresponding to seqid as a string. start/stop are in sequence coordinates. Excludes gaps.
get_view
core.seq_storage.SeqsData.get_view(seqid)reurns view of sequence data for seqid