diff --git a/mutalyzer/grammar.py b/mutalyzer/grammar.py
index f2a1b830bd24066753607abc743c3e21616fcfed..a8a987d110ed7c4dc95b7cf78cccb71393aa6f7d 100644
--- a/mutalyzer/grammar.py
+++ b/mutalyzer/grammar.py
@@ -205,8 +205,9 @@ class Grammar():
Suppress(']')) ^ (RangeLoc + Suppress('[') + Number + \
Suppress(']')) ^ AbrSSR
- # BNF: Seq -> (Nt+ | Number | RangeLoc | FarLoc) Nest?
- Seq = Group(NtString('Sequence') ^ Number ^ RangeLoc('Range') ^ \
+ # BNF: Seq -> (Nt+ | Number | RangeLoc `inv'? | FarLoc) Nest?
+ Seq = Group(NtString('Sequence') ^ Number ^ \
+ (RangeLoc('Range') + Optional(Literal('inv')('Inv'))) ^ \
FarLoc('OptRef') + Optional(Nest))('Seq')
# BNF: SeqList -> Seq (`;' Seq)*
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 18412996209a1d388c3954b9913b758bb6fd9daf..82a7cbb9b74412ea48ceebc494a4ab2ed14ef553 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1228,7 +1228,11 @@ def process_raw_variant(mutator, variant, record, transcript, output):
'Position %s is out of range.' % range_last)
raise _RawVariantError()
- return mutator.orig[range_first - 1:range_last]
+ insertion = mutator.orig[range_first - 1:range_last]
+ if seq.Inv:
+ insertion = Bio.Seq.reverse_complement(str(insertion))
+
+ return insertion
output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
'Only the insertion of a sequence or a range is '
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 4072549e3581db9656131d7d3ef8af2e7d6618fc..98bd76f330e5e3aa6ff34e4b11a6d4fa5d326ec0 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -54,6 +54,11 @@ class TestGrammar(MutalyzerTest):
self._parse('NM_002001.2:c.15_16ins[28_39;A]')
self._parse('NM_002001.2:c.15_16ins[28_39;ATC]')
self._parse('NM_002001.2:c.15_16ins[28_39;A;ATC]')
+ self._parse('NM_002001.2:c.15_16ins28_39inv')
+ self._parse('NM_002001.2:c.15_16ins[28_39inv]')
+ self._parse('NM_002001.2:c.15_16ins[28_39inv;A]')
+ self._parse('NM_002001.2:c.15_16ins[28_39inv;ATC]')
+ self._parse('NM_002001.2:c.15_16ins[28_39inv;A;ATC]')
def test_compound_delins(self):
"""
@@ -68,6 +73,11 @@ class TestGrammar(MutalyzerTest):
self._parse('NM_002001.2:c.12_17delins[28_39;A]')
self._parse('NM_002001.2:c.12_17delins[28_39;ATC]')
self._parse('NM_002001.2:c.12_17delins[28_39;A;ATC]')
+ self._parse('NM_002001.2:c.12_17delins28_39inv')
+ self._parse('NM_002001.2:c.12_17delins[28_39inv]')
+ self._parse('NM_002001.2:c.12_17delins[28_39inv;A]')
+ self._parse('NM_002001.2:c.12_17delins[28_39inv;ATC]')
+ self._parse('NM_002001.2:c.12_17delins[28_39inv;A;ATC]')
def test_protein_variants(self):
"""
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 4f4351585aaee48120032f63090ade94f83887e4..bd33d09dde2ea59e9db9b89ae59112da3601bccd 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -579,6 +579,18 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_inv(self):
+ """
+ Insertion of an inverse range.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins4300_4320inv', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGCCAGATAATGAGCACAGGAC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGCCAGATAATGAGCACAGGAC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_ins_seq_list(self):
"""
@@ -613,6 +625,18 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_inv_list(self):
+ """
+ Insertion of an inverse range as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4320inv]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGCCAGATAATGAGCACAGGAC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGCCAGATAATGAGCACAGGAC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_ins_seq_seq(self):
"""
@@ -647,6 +671,18 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_range_inv(self):
+ """
+ Insertion of a range and an inverse range.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4309;4310_4320inv]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTGCCAGATAATG')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTGCCAGATAATG' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_ins_seq_range(self):
"""
@@ -658,6 +694,17 @@ class TestVariantchecker(MutalyzerTest):
assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_range_inv(self):
+ """
+ Insertion of a sequence and an inverse range.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[GTCCTGTGCT;4310_4320inv]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTGCCAGATAATG')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTGCCAGATAATG' \
+ in self.output.getOutput('descriptions')
+
@fix(cache('NG_008939.1'))
def test_ins_range_seq(self):
"""
@@ -669,6 +716,17 @@ class TestVariantchecker(MutalyzerTest):
assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_inv_seq(self):
+ """
+ Insertion of an inverse range and a sequence.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4309inv;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insAGCACAGGACCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insAGCACAGGACCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
@fix(cache('NG_008939.1'))
def test_ins_seq_coding(self):
"""
@@ -710,6 +768,14 @@ class TestVariantchecker(MutalyzerTest):
check_variant('NG_008939.1(PCCB_v001):c.156_157ins180_188', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_inv_coding(self):
+ """
+ Insertion of an inverse range (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157ins180_188inv', self.output)
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+
@fix(cache('NG_008939.1'))
def test_ins_range_list_coding(self):
"""
@@ -718,6 +784,14 @@ class TestVariantchecker(MutalyzerTest):
check_variant('NG_008939.1(PCCB_v001):c.156_157ins[180_188]', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_inv_list_coding(self):
+ """
+ Insertion of an inverse range as a list (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157ins[180_188inv]', self.output)
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+
@fix(cache('NG_008939.1'))
def test_delins_seq(self):
"""
@@ -741,6 +815,18 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv(self):
+ """
+ Insertion-deletion of an inverse range.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins4300_4320inv', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGCCAGATAATGAGCACAGGAC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGCCAGATAATGAGCACAGGAC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_delins_seq_list(self):
"""
@@ -764,6 +850,18 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv_list(self):
+ """
+ Insertion-deletion of an inverse range as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4320inv]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGCCAGATAATGAGCACAGGAC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGCCAGATAATGAGCACAGGAC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_delins_seq_seq(self):
"""
@@ -787,6 +885,20 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv_range(self):
+ """
+ Insertion-deletion of an inverse range and a range.
+
+ Note that the delins is also shortened by one position here.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4309inv;4310_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5208_5212delinsGCACAGGACCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.157_161delinsGCACAGGACCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
@fix(cache('NG_008939.1'))
def test_delins_seq_range(self):
"""
@@ -798,6 +910,19 @@ class TestVariantchecker(MutalyzerTest):
assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_range_inv(self):
+ """
+ Insertion-deletion of a sequence and an inverse range.
+
+ Note that the delins is also shortened by one position here.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[GTCCTGTGCT;4310_4320inv]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5211delinsGTCCTGTGCTGCCAGATAAT')
+ assert 'NG_008939.1(PCCB_v001):c.156_160delinsGTCCTGTGCTGCCAGATAAT' \
+ in self.output.getOutput('descriptions')
+
@fix(cache('NG_008939.1'))
def test_delins_range_seq(self):
"""
@@ -809,6 +934,19 @@ class TestVariantchecker(MutalyzerTest):
assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
in self.output.getOutput('descriptions')
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv_seq(self):
+ """
+ Insertion-deletion of an inverse range and a sequence.
+
+ Note that the delins is also shortened by one position here.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4309inv;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5208_5212delinsGCACAGGACCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.157_161delinsGCACAGGACCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
@fix(cache('NG_008939.1'))
def test_delins_seq_coding(self):
"""
@@ -850,6 +988,14 @@ class TestVariantchecker(MutalyzerTest):
check_variant('NG_008939.1(PCCB_v001):c.156_161delins180_188', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv_coding(self):
+ """
+ Insertion-deletion of an inverse range (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delins180_188inv', self.output)
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+
@fix(cache('NG_008939.1'))
def test_delins_range_list_coding(self):
"""
@@ -858,6 +1004,14 @@ class TestVariantchecker(MutalyzerTest):
check_variant('NG_008939.1(PCCB_v001):c.156_161delins[180_188]', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_inv_list_coding(self):
+ """
+ Insertion-deletion of an inverse range as a list (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delins[180_188inv]', self.output)
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
+
def test_no_reference(self):
"""
Variant description without a reference.