Remove Beacon Translator

[korikuzma]

Remove Beacon Translator (and all references to Beacon)

vrs-python/src/ga4gh/vrs/extras/translator.py

Lines 218 to 278 in b573565

	@deprecated("This method does not match the Beacon spec and will be removed in v3.")
	def _from_beacon(self, beacon_expr: str, **kwargs) -> models.Allele | None:
	"""Parse beacon expression into VRS Allele
	kwargs:
	assembly_name (str): Assembly used for `beacon_expr`.
	rle_seq_limit Optional(int): If RLE is set as the new state after
	normalization, this sets the limit for the length of the `sequence`.
	To exclude `sequence` from the response, set to 0.
	For no limit, set to `None`.
	Defaults value set in instance variable, `rle_seq_limit`.
	do_normalize (bool): `True` if fully justified normalization should be
	performed. `False` otherwise. Defaults to `True`
	#>>> a = tlr.from_beacon("19 : 44908822 C > T")
	#>>> a.model_dump()
	{
	'location': {
	'end': 44908822,
	'start': 44908821,
	'sequenceReference': {
	'type': 'SequenceReference',
	'refgetAccession': 'SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl'
	},
	'type': 'SequenceLocation'
	},
	'state': {
	'sequence': 'C',
	'type': 'LiteralSequenceExpression'
	},
	'type': 'Allele'
	}
	"""
	if not isinstance(beacon_expr, str):
	return None
	m = self.beacon_re.match(beacon_expr.replace(" ", ""))
	if not m:
	return None
	g = m.groupdict()
	assembly_name = kwargs.get("assembly_name", self.default_assembly_name)
	sequence = assembly_name + ":" + g["chr"]
	refget_accession = self.data_proxy.derive_refget_accession(sequence)
	if not refget_accession:
	return None
	start = int(g["pos"]) - 1
	ref = g["ref"]
	alt = g["alt"]
	end = start + len(ref)
	ins_seq = alt
	values = {
	"refget_accession": refget_accession,
	"start": start,
	"end": end,
	"literal_sequence": ins_seq,
	}
	return self._create_allele(values, **kwargs)

In #568 (PR #578) we added a deprecation warning that the translator does not match the Beacon spec and will be removed in v3.