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Also handle insertions
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b0d0nne11 committed Jan 5, 2024
1 parent 0e4eeb2 commit c2408ba
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Showing 4 changed files with 13 additions and 2 deletions.
2 changes: 1 addition & 1 deletion src/hgvs/utils/altseqbuilder.py
Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ def _get_variant_region(self):
):
result = self.T_UTR
elif (
self._var_c.posedit.edit.type == "dup"
self._var_c.posedit.edit.type in ["dup", "ins"]
and self._var_c.posedit.pos.end.datum == Datum.CDS_END
):
result = self.T_UTR
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Binary file modified tests/data/cache-py3.hdp
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6 changes: 6 additions & 0 deletions tests/test_hgvs_variantmapper.py
Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,12 @@ def test_map_of_c_out_of_reference_bound(self):
with pytest.raises(HGVSError, match="coordinate is out of bounds"):
self.vm.c_to_p(var_c)

def test_map_of_ins_three_prime_utr(self):
hgvs_c = "NM_004985.4:c.567_*1insCCC"
var_c = self.hp.parse_hgvs_variant(hgvs_c)
var_p = self.vm.c_to_p(var_c)
self.assertEqual(str(var_p), "NP_004976.2:p.?")

def test_map_of_dup_three_prime_utr(self):
hgvs_c = "NM_153223.3:c.2959_*1dup"
var_c = self.hp.parse_hgvs_variant(hgvs_c)
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7 changes: 6 additions & 1 deletion tests/test_hgvs_variantmapper_cp_sanity.py
Original file line number Diff line number Diff line change
Expand Up @@ -159,11 +159,16 @@ def test_five_prime_utr(self):
hgvsp_expected = "MOCK:p.?"
self._run_conversion(hgvsc, hgvsp_expected)

def test_three_prime_utr(self):
def test_sub_three_prime_utr(self):
hgvsc = "NM_999999.1:c.*3G>A"
hgvsp_expected = "MOCK:p.?"
self._run_conversion(hgvsc, hgvsp_expected)

def test_ins_three_prime_utr(self):
hgvsc = "NM_999999.1:c.39_*1insA"
hgvsp_expected = "MOCK:p.?"
self._run_conversion(hgvsc, hgvsp_expected)

def test_dup_three_prime_utr(self):
hgvsc = "NM_999999.1:c.12_*1dup"
hgvsp_expected = "MOCK:p.?"
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