def deserialise_seq(data, aligned=False):
"""deserialises sequence and any annotations
Parameters
----------
data : dict
a result of json.loads of a to_rich_dict()
aligned
whether sequence type is for an Alignment, in which case an Aligned
instance will be returned
Returns
-------
"""
from cogent3.core.moltype import get_moltype
data.pop("version", None)
data["moltype"] = get_moltype(data.pop("moltype"))
annotations = data.pop("annotations", None)
make_seq = data["moltype"].make_seq
_ = data.pop("type")
if "-" in data["seq"]:
aligned = True
data.pop("moltype")
result = make_seq(**data)
if aligned:
map_, result = result.parse_out_gaps()
if annotations:
deserialise_annotation(annotations, result)
if aligned:
result = Aligned(map_, result)
return result
def make_aligned(gaps_lengths, seq, name="seq1"):
seq = seq.moltype.make_seq(seq, name=name)
return Aligned(gap_coords_to_map(gaps_lengths, len(seq)), seq)