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Description
Describe the bug
I get an error message of AttributeError: 'AARefAlt' object has no attribute 'ref_n'
when using validate()
against a protein variant.
To Reproduce
Steps to reproduce the behavior, invoke hgvs-shell
(v1.5.4):
hgvs_t = hp.parse_hgvs_variant('NM_001330729.1(CTNNB1):c.15_398del')
hgvs_p = c_to_p(hgvs_t)
validate(hgvs_p)
It raised the error:
AttributeError: 'AARefAlt' object has no attribute 'ref_n'
Expected behavior
I expect a boolean returned value.
Additional context
The traceback pointed the error to posedit.py
:
101 # Check del length
102 if self.edit.type in ["del", "delins"]:
--> 103 ref_len = self.edit.ref_n
104 if ref_len is not None and ref_len != self.pos.end - self.pos.start + 1:
105 return (
106 ValidationLevel.ERROR,
107 "Length implied by coordinates must equal sequence deletion length",
108 )
It seems we can solve the problem by adding ref_n
to AARefAltdecorated by
@property`. I made a patch at here. It fixes the problem from my side, but am not sure if it fits well to the whole package. Thanks!