Parse uncertain c.HGVS names #801
Description
Looking in the parser syntax (hgvs.pymeta) most of the uncertainty is only applied for g. ie uncertain_g_interval - hopefully we just need to copy it for c. but here's what's currently happening:
C_UNCERTAIN_EXAMPLES = [
"NM_000333.3:c.(4_246)del",
"NM_000333.3:c.(4_6)_246del",
"NM_000333.3:c.4_(245_246)del",
"NM_000333.3:c.(4_6)_(245_246)del",
"NM_000333.3:c.(?_6)_245del",
"NM_000333.3:c.4_(245_?)del",
"NM_000333.3:c.(?_6)_(245_?)del",
]
for hgvs_name in C_UNCERTAIN_EXAMPLES:
try:
parse(hgvs_name)
print(f"{hgvs_name} -> OK")
except Exception as e:
print(f"{hgvs_name} -> {e}")
NM_000333.3:c.(4_246)del -> OK
NM_000333.3:c.(4_6)_246del -> NM_000333.3:c.(4_6)_246del: char 19: expected one of '=', 'con', 'copy', 'del', 'dup', 'ins', or 'inv'
NM_000333.3:c.4_(245_246)del -> NM_000333.3:c.4_(245_246)del: char 16: expected one of '*', or a digit
NM_000333.3:c.(4_6)_(245_246)del -> NM_000333.3:c.(4_6)_(245_246)del: char 19: expected one of '=', 'con', 'copy', 'del', 'dup', 'ins', or 'inv'
NM_000333.3:c.(?_6)_245del -> NM_000333.3:c.(?_6)_245del: char 15: expected one of '*', or a digit
NM_000333.3:c.4_(245_?)del -> NM_000333.3:c.4_(245_?)del: char 16: expected one of '*', or a digit
NM_000333.3:c.(?_6)_(245_?)del -> NM_000333.3:c.(?_6)_(245_?)del: char 15: expected one of '*', or a digit
There are some c.HGVS examples from ClinVar here