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Other ambiguities
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@mihailefter
mihailefter committed Aug 2, 2023
1 parent e3edd25 commit dcb8c47
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164 changes: 161 additions & 3 deletions mutalyzer_hgvs_parser/hgvs_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,8 +257,8 @@
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")
and len(get_child(children, [2, 0]).children) == 1
),
"selected": 2,
},
Expand Down Expand Up @@ -295,6 +295,164 @@
),
"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")

),
"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")
),
"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")
),
"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")
),
"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")
),
"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")
),
"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")
),
"selected": 2
},
]


Expand All @@ -303,8 +461,8 @@ def _ambig(self, children):
for ambig in AMBIGUITIES:
if ambig["conditions"](children):
return children[ambig["selected"]]
# from lark.tree import pydot__tree_to_png
# pydot__tree_to_png(Tree("ambig", children), "ambig.png")
from lark.tree import pydot__tree_to_png
pydot__tree_to_png(Tree("ambig", children), "ambig.png")
raise Exception("Ambiguity not solved.")


Expand Down
56 changes: 55 additions & 1 deletion tests/test_convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -959,6 +959,53 @@ def test_variants_to_model(variants, model):
]
}],
},
"R1:c.10-5_10-2delinsTCTR2.2:c.10": {
"reference": REFERENCES["R1"],
"type": "description_dna",
"coordinate_system": "c",
"variants": [{
"location": LOCATIONS["10-5_10-2"],
"type": "deletion_insertion",
"source": "reference",
"inserted": [
{
"type": "description_dna",
"source": {"id": "TCTR2.2"},
"coordinate_system": "c",
"location": {
"type": "point",
"position": 10
}
}
]
}],
},
# TODO: revisit this in the repeats context.
"R1:c.10-20[5]": {
"reference": REFERENCES["R1"],
"type": "description_dna",
"coordinate_system": "c",
"variants": [{
"location": LOCATIONS["10-20"],
"type": "repeat",
"source": "reference",
"inserted": [{"length": LENGTHS["5"]}
]
}],
},
"R1:c.10-5_10-2[5]": {
"reference": REFERENCES["R1"],
"type": "description_dna",
"coordinate_system": "c",
"variants": [{
"location": LOCATIONS["10-5_10-2"],
"type": "repeat",
"source": "reference",
"inserted": [{"length": LENGTHS["5"]}
]
}],
},

}


Expand Down Expand Up @@ -1012,7 +1059,14 @@ def test_mix(description, model):

@pytest.mark.parametrize(
"description",
["R1:1delinsR2:2del", "R1:1del[R2:2del]", "R1:[1del;10_11insR2:2del]"],
[
"R1:1delinsR2:2del",
"R1:1del[R2:2del]",
"R1:[1del;10_11insR2:2del]",
"R1:c.10-5_10-2delR2:10del",
"R1:c.10-5_10-2dupR2:10del",
"R1:c.10-5_10-2delinsTCTR2.2:c.10insT",
],
)
def test_nested_descriptions(description):
with pytest.raises(NestedDescriptions):
Expand Down

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