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Fix other ambiguities
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@mihailefter
mihailefter committed Nov 19, 2024
1 parent 08bc90a commit ef7d0a1
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316 changes: 175 additions & 141 deletions mutalyzer_hgvs_parser/hgvs_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,207 +269,239 @@
"type": "variant_certain-location_repeat|repeat - variant_certain-location",
# NM_000492.4:c.1210-34_1210-6
"conditions": lambda children: (
len(children) == 3
and children[0].data == children[1].data == children[2].data == "variant_certain"
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 1
and data_equals(children, [2, 0], "location")
len(children) == 3
and children[0].data == children[1].data == children[2].data == "variant_certain"
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 1
and data_equals(children, [2, 0], "location")
),
"selected": 2,
},
{
"type": "variant_certain-location_repeat|location_inversion - inversion",
# NC_000015.9(NM_001012338.3):c.396-6644_1397-29766inv
"conditions": lambda children: (
len(children) == 3
and children[0].data == children[1].data == children[2].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "inversion")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")
len(children) == 3
and children[0].data == children[1].data == children[2].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "inversion")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")
),
"selected": 0,
},
{
"type": "variant_certain_duplication | variant_certain_repeat - duplication",
# R1:c.10-5_10-2dupR2:10
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "duplication")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "duplication")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
),
"selected": 0,
},
{
"type": "variant_certain_deletion | variant_certain_repeat - deletion",
# R1:c.10-5_10-2delR2:10del
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "deletion")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")

len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "deletion")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")
),
"selected": 0,
},
{
"type": "variant_certain_delins | variant_certain_delins - one insert",
# R1:c.10-5_10-2delinsTCTR2.2:c.10insT
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "deletion_insertion"
and len(get_child(children, [1]).children) == 1
and data_equals(children, [0, 0], "inserted")
len(children) == 2
and children[0].data == children[1].data == "deletion_insertion"
and len(get_child(children, [1]).children) == 1
and data_equals(children, [0, 0], "inserted")
),
"selected": 1
"selected": 1,
},
# TODO: revisit the next ones in the repeats context.
{
"type": "variant_certain_repeat | variant_certain_repeat_length - length 0",
# R1:c.10-2[5]
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")

and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")
and len(get_child(children, [0, 1, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0], "insert")
and len(get_child(children, [0, 1, 0, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0, 0], "length")
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")
and len(get_child(children, [0, 1, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0], "insert")
and len(get_child(children, [0, 1, 0, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0, 0], "length")
),
"selected": 0
"selected": 0,
},
{
"type": "variant_certain_repeat | variant_certain_repeat_length - length 1",
# R1:c.10-2[5]
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")

and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [1, 1]).children) == 1
and data_equals(children, [1, 1, 0], "inserted")
and len(get_child(children, [1, 1, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0], "insert")
and len(get_child(children, [1, 1, 0, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0, 0], "length")
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [1, 1]).children) == 1
and data_equals(children, [1, 1, 0], "inserted")
and len(get_child(children, [1, 1, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0], "insert")
and len(get_child(children, [1, 1, 0, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0, 0], "length")
),
"selected": 1
"selected": 1,
},
{
"type": "variant_certain_repeat | variant_certain_repeat_range_length - length 0",
# R1:c.10-2_10-4[5]
"conditions": lambda children: (
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")

and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")

and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")
and len(get_child(children, [0, 1, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0], "insert")
and len(get_child(children, [0, 1, 0, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0, 0], "length")
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")
and len(get_child(children, [0, 1]).children) == 1
and data_equals(children, [0, 1, 0], "inserted")
and len(get_child(children, [0, 1, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0], "insert")
and len(get_child(children, [0, 1, 0, 0]).children) == 1
and data_equals(children, [0, 1, 0, 0, 0], "length")
),
"selected": 0
"selected": 0,
},
{
"type": "variant_certain_repeat | variant_certain_repeat_range_length - length 1",
# R1:c.10-2_10-4[5]
"conditions": lambda children: (
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")

and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")

and len(get_child(children, [1, 1]).children) == 1
and data_equals(children, [1, 1, 0], "inserted")
and len(get_child(children, [1, 1, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0], "insert")
and len(get_child(children, [1, 1, 0, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0, 0], "length")
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")
and len(get_child(children, [1, 1]).children) == 1
and data_equals(children, [1, 1, 0], "inserted")
and len(get_child(children, [1, 1, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0], "insert")
and len(get_child(children, [1, 1, 0, 0]).children) == 1
and data_equals(children, [1, 1, 0, 0, 0], "length")
),
"selected": 1
"selected": 1,
},
{
"type": "variant_certain_repeat | variant_certain_repeat_range_length - length 2",
# R1:c.10-2_10-4[5]
"conditions": lambda children: (
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")

and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")

and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")

and len(get_child(children, [2, 1]).children) == 1
and data_equals(children, [2, 1, 0], "inserted")
and len(get_child(children, [2, 1, 0]).children) == 1
and data_equals(children, [2, 1, 0, 0], "insert")
and len(get_child(children, [2, 1, 0, 0]).children) == 1
and data_equals(children, [2, 1, 0, 0, 0], "length")
len(children) == 3
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and data_equals(children, [1, 1], "repeat")
and len(get_child(children, [2]).children) == 2
and data_equals(children, [2, 0], "location")
and data_equals(children, [2, 1], "repeat")
and len(get_child(children, [2, 1]).children) == 1
and data_equals(children, [2, 1, 0], "inserted")
and len(get_child(children, [2, 1, 0]).children) == 1
and data_equals(children, [2, 1, 0, 0], "insert")
and len(get_child(children, [2, 1, 0, 0]).children) == 1
and data_equals(children, [2, 1, 0, 0, 0], "length")
),
"selected": 2
"selected": 2,
},
{
"type": "variant_certain_repeat | variant_certain_substitution - 2",
# for protein descriptions
# STR:D5S818
"conditions": lambda children: (
len(children) == 2
and children[0].data == children[1].data == "variant_certain"
and len(get_child(children, [0]).children) == 2
and data_equals(children, [0, 0], "location")
and isinstance(get_child(children, [0, 0, 0]), Tree)
and data_equals(children, [0, 0, 0], "point")
and len(get_child(children, [0, 0, 0]).children) == 2
and isinstance(get_child(children, [0, 0, 0, 0]), Token)
and isinstance(get_child(children, [0, 0, 0, 1]), Token)
and data_equals(children, [0, 1], "repeat")
and len(get_child(children, [1]).children) == 2
and data_equals(children, [1, 0], "location")
and isinstance(get_child(children, [1, 0, 0]), Tree)
and data_equals(children, [1, 0, 0], "point")
and len(get_child(children, [1, 0, 0]).children) == 2
and isinstance(get_child(children, [1, 0, 0, 0]), Token)
and isinstance(get_child(children, [1, 0, 0, 1]), Token)
and data_equals(children, [1, 1], "substitution")
),
"selected": 1,
},
{
"type": "deletion_insertion | deletion_insertion | ... nested - 0",
# REF_1:10del REF_2:20insA REF_3:30insT
"conditions": lambda children: (
len(children) >= 2
and children[0].data == children[1].data == "deletion_insertion"
and len(get_child(children, [0]).children) == 2
and len(get_child(children, [1]).children) == 2
and isinstance(get_child(children, [1, 0]), Tree)
and len(get_child(children, [1, 0]).children) == 1
and isinstance(get_child(children, [1, 1]), Tree)
and len(get_child(children, [1, 1]).children) == 1
and data_equals(children, [1, 0, 0], "insert")
and len(get_child(children, [1, 0, 0]).children) == 1
and (
data_equals(children, [1, 0, 0, 0], "description_dna")
or data_equals(children, [1, 0, 0, 0], "description_protein")
)
),
"selected": 1,
},
]

Expand Down Expand Up @@ -698,10 +730,12 @@ def status(self):
" Propagate positions: %s" % self._parser.options.propagate_positions
)


@functools.lru_cache
def get_parser(grammar_path=None, start_rule=None):
return HgvsParser(grammar_path, start_rule)


def parse(description, grammar_path=None, start_rule=None):
"""
Parse the provided HGVS `description`, or the description part,
Expand Down
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