Remove Beacon Translator

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.

feat!: remove beacon translator

feat!: remove beacon translator (#625)

Completed in #625

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Remove Beacon Translator #622

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	@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)

Remove Beacon Translator #622

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theferrit32 commented on Apr 15, 2026

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