diff --git a/mutalyzer/grammar.py b/mutalyzer/grammar.py
index 49388f75d8f4ed2de9f35076deea5559d98cfd01..f2a1b830bd24066753607abc743c3e21616fcfed 100644
--- a/mutalyzer/grammar.py
+++ b/mutalyzer/grammar.py
@@ -205,18 +205,26 @@ class Grammar():
Suppress(']')) ^ (RangeLoc + Suppress('[') + Number + \
Suppress(']')) ^ AbrSSR
- # BNF: Ins -> RangeLoc `ins' (Nt+ | Number | RangeLoc | FarLoc) Nest?
- Ins = RangeLoc + Literal('ins')('MutationType') + \
- ((NtString ^ Number)('Arg1') ^ RangeLoc ^ \
- FarLoc('OptRef')) + Optional(Nest)
+ # BNF: Seq -> (Nt+ | Number | RangeLoc | FarLoc) Nest?
+ Seq = Group(NtString('Sequence') ^ Number ^ RangeLoc('Range') ^ \
+ FarLoc('OptRef') + Optional(Nest))('Seq')
+
+ # BNF: SeqList -> Seq (`;' Seq)*
+ SeqList = delimitedList(Seq, delim=';')('SeqList')
+
+ # BNF: SimpleSeqList -> (`[' SeqList `]') | Seq
+ SimpleSeqList = Suppress('[') + SeqList + Suppress(']') ^ Seq
+
+ # BNF: Ins -> RangeLoc `ins' SimpleSeqList
+ Ins = RangeLoc + Literal('ins')('MutationType') + SimpleSeqList
# BNF: Indel -> (RangeLoc | PtLoc) `del' (Nt+ | Number)?
- # `ins' (Nt+ | Number | RangeLoc | FarLoc) Nest?
+ # `ins' SimpleSeqList
# Note that the alternative PtLoc is not included in [3].
Indel = (RangeLoc ^ Group(PtLoc('PtLoc'))('StartLoc')) + Literal('del') + \
Optional(NtString ^ Number)('Arg1') + \
Literal('ins').setParseAction(replaceWith('delins'))('MutationType') + \
- ((NtString ^ Number)('Arg2') ^ RangeLoc ^ FarLoc) + Optional(Nest)
+ SimpleSeqList
# BNF: Inv -> RangeLoc `inv' (Nt+ | Number)? Nest?
Inv = RangeLoc + Literal('inv')('MutationType') + \
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index ed751d0829728a814a900ea96112a56712ff5cdb..9a059a68441631c6a645d2c93201385e2ab80372 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -56,10 +56,27 @@ def _construct_change(var, reverse=False):
arg1 = var.Arg1
arg2 = var.Arg2
+ def parse_sequence(seq):
+ if not seq.Sequence:
+ raise NotImplementedError('Only explicit sequences are supported '
+ 'for insertions.')
+ if reverse:
+ return reverse_complement(str(seq.Sequence))
+ return seq.Sequence
+
if var.MutationType == 'subst':
change = '%s>%s' % (arg1, arg2)
- elif var.MutationType == 'delins' and arg2:
- change = '%s%s' % (var.MutationType, arg2)
+ elif var.MutationType in ('ins', 'delins'):
+ if var.SeqList:
+ if reverse:
+ seqs = reversed(var.SeqList)
+ else:
+ seqs = var.SeqList
+ insertion = '[' + ';'.join(str(parse_sequence(seq))
+ for seq in seqs) + ']'
+ else:
+ insertion = parse_sequence(var.Seq)
+ change = '%s%s' % (var.MutationType, insertion)
else:
change = '%s%s' % (var.MutationType, arg1 or arg2 or '')
@@ -506,8 +523,14 @@ class Converter(object) :
# Construct the variant descriptions
descriptions = []
for variant, mapping in zip(variants, mappings):
- f_change = _construct_change(variant)
- r_change = _construct_change(variant, reverse=True)
+ try:
+ f_change = _construct_change(variant)
+ r_change = _construct_change(variant, reverse=True)
+ except NotImplementedError as e:
+ self.__output.addMessage(__file__, 3, 'ENOTIMPLEMENTED',
+ str(e))
+ return None
+
if self.mapping.orientation == 'forward':
change = f_change
else :
@@ -723,8 +746,13 @@ class Converter(object) :
mutations = []
for variant, cmap in zip(variants, core_mapping):
- f_change = _construct_change(variant)
- r_change = _construct_change(variant, reverse=True)
+ try:
+ f_change = _construct_change(variant)
+ r_change = _construct_change(variant, reverse=True)
+ except NotImplementedError as e:
+ self.__output.addMessage(__file__, 4,
+ "ENOTIMPLEMENTEDERROR", str(e))
+ return None
startp = self.crossmap.tuple2string((cmap.startmain, cmap.startoffset))
endp = self.crossmap.tuple2string((cmap.endmain, cmap.endoffset))
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 30bbbfc226f5aa4ccb7cd4c1078c542229c45ac8..18412996209a1d388c3954b9913b758bb6fd9daf 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1185,25 +1185,74 @@ def process_raw_variant(mutator, variant, record, transcript, output):
if variant.MutationType == 'inv':
apply_inversion(first, last, mutator, record, output)
- # Insertion.
- if variant.MutationType == 'ins':
- # Check if the inserted sequence is not a range.
- # Todo: Implement this feature.
- if not argument:
- output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
- 'Insertion of a range is not implemented yet.')
- raise _RangeInsertionError()
- apply_insertion(first, last, argument, mutator, record, output)
-
- # DelIns.
- if variant.MutationType == 'delins':
- # Check if the inserted sequence is not a range.
- # Todo: Implement this feature.
- if not sequence:
- output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
- 'Insertion of a range is not implemented yet.')
- raise _RangeInsertionError()
- apply_delins(first, last, sequence, mutator, record, output)
+ # Parse a Seq object containing a Sequence or a Range into a string.
+ def parse_sequence(seq):
+ if seq.Sequence:
+ if transcript and transcript.CM.orientation == -1:
+ return Bio.Seq.reverse_complement(str(seq.Sequence))
+ return seq.Sequence
+
+ if seq.StartLoc and seq.EndLoc:
+ if transcript:
+ output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
+ 'The insertion of a range is only supported '
+ 'with genomic positioning.')
+ raise _RangeInsertionError()
+
+ try:
+ range_first, range_last = _genomic_to_genomic(
+ seq.StartLoc.PtLoc, seq.EndLoc.PtLoc)
+ except _UnknownPositionError:
+ output.addMessage(__file__, 4, 'EUNKNOWN',
+ 'Unknown positions (denoted by "?") are '
+ 'not supported.')
+ raise
+ except _RawVariantError:
+ output.addMessage(__file__, 4, 'EPOSITION',
+ 'Could not determine range.')
+ raise
+
+ if range_last < range_first:
+ output.addMessage(__file__, 3, 'ERANGE',
+ 'End position is smaller than the begin '
+ 'position.')
+ raise _RawVariantError()
+
+ if range_first < 1:
+ output.addMessage(__file__, 4, 'ERANGE',
+ 'Position %i is out of range.' % range_first)
+ raise _RawVariantError()
+
+ if range_last > len(mutator.orig):
+ output.addMessage(__file__, 4, 'ERANGE',
+ 'Position %s is out of range.' % range_last)
+ raise _RawVariantError()
+
+ return mutator.orig[range_first - 1:range_last]
+
+ output.addMessage(__file__, 4, 'ENOTIMPLEMENTED',
+ 'Only the insertion of a sequence or a range is '
+ 'implemented.')
+ raise _RawVariantError()
+
+ if variant.MutationType in ('ins', 'delins'):
+ if variant.SeqList:
+ if transcript and transcript.CM.orientation == -1:
+ seqs = reversed(variant.SeqList)
+ else:
+ seqs = variant.SeqList
+ insertion = ''.join(str(parse_sequence(seq))
+ for seq in seqs)
+ else:
+ insertion = parse_sequence(variant.Seq)
+
+ # Insertion.
+ if variant.MutationType == 'ins':
+ apply_insertion(first, last, insertion, mutator, record, output)
+
+ # DelIns.
+ if variant.MutationType == 'delins':
+ apply_delins(first, last, insertion, mutator, record, output)
#process_raw_variant
diff --git a/tests/fixtures.py b/tests/fixtures.py
index e25d018dc5b5b2392cb5170bd42bcae47063b4a1..595d72a663e3ec06a6df748f3d21e6aa4a8019ee 100644
--- a/tests/fixtures.py
+++ b/tests/fixtures.py
@@ -245,6 +245,21 @@ def hg19_transcript_mappings():
cds=(111957632, 111965694),
select_transcript=False,
version=2))
+ session.add(TranscriptMapping(
+ chromosome_11,
+ 'refseq',
+ 'NM_012459',
+ 'TIMM8B',
+ 'reverse',
+ 111955524,
+ 111957522,
+ [111955524, 111957364],
+ [111956186, 111957522],
+ 'ncbi',
+ transcript=1,
+ cds=(111956019, 111957492),
+ select_transcript=False,
+ version=2))
session.add(TranscriptMapping(
chromosome_11,
'refseq',
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index f9bf9ec9c637355bfa8abcef5a73afc353b8b38f..4072549e3581db9656131d7d3ef8af2e7d6618fc 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -41,6 +41,34 @@ class TestGrammar(MutalyzerTest):
self._parse('NM_002001.2:c.[(12del;12del)]')
self._parse('NM_002001.2:c.[((12del)?;12del)?]')
+ def test_compound_insertion(self):
+ """
+ Some some compound insertions.
+ """
+ self._parse('NM_002001.2:c.15_16insA')
+ self._parse('NM_002001.2:c.15_16insATC')
+ self._parse('NM_002001.2:c.15_16ins[A]')
+ self._parse('NM_002001.2:c.15_16ins[ATC]')
+ self._parse('NM_002001.2:c.15_16ins28_39')
+ self._parse('NM_002001.2:c.15_16ins[28_39]')
+ 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]')
+
+ def test_compound_delins(self):
+ """
+ Some some compound deletion-insertions.
+ """
+ self._parse('NM_002001.2:c.12_17delinsA')
+ self._parse('NM_002001.2:c.12_17delinsATC')
+ self._parse('NM_002001.2:c.12_17delins[A]')
+ self._parse('NM_002001.2:c.12_17delins[ATC]')
+ self._parse('NM_002001.2:c.12_17delins28_39')
+ self._parse('NM_002001.2:c.12_17delins[28_39]')
+ 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]')
+
def test_protein_variants(self):
"""
Some protein variants.
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 4b2af7d4107dd44309012ee0f40ebbd5dcd2d8f1..3acb53cbd279f113888a2582741e8ed91736a798 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -301,3 +301,37 @@ class TestConverter(MutalyzerTest):
genomic = converter.c2chrom('NM_017780.2(CHD8):c.109A>T')
erange = self.output.getMessagesWithErrorCode('EACCNOTINDB')
assert_equal(len(erange), 1)
+
+ def test_ins_seq_chrom2c(self):
+ """
+ Insertion of a sequence (chrom2c).
+ """
+ converter = self._converter('hg19')
+ coding = converter.chrom2c('NC_000011.9:g.111957482_111957483insGAT', 'list')
+ assert 'NM_003002.2:c.-150_-149insGAT' in coding
+ assert 'NM_012459.2:c.10_11insATC' in coding
+
+ def test_ins_seq_seq(self):
+ """
+ Insertion of two sequences (chrom2c).
+ """
+ converter = self._converter('hg19')
+ coding = converter.chrom2c('NC_000011.9:g.111957482_111957483ins[GAT;AAA]', 'list')
+ assert 'NM_003002.2:c.-150_-149ins[GAT;AAA]' in coding
+ assert 'NM_012459.2:c.10_11ins[TTT;ATC]' in coding
+
+ def test_ins_seq_c2chrom_reverse(self):
+ """
+ Insertion of a sequence on reverse strand (c2chrom).
+ """
+ converter = self._converter('hg19')
+ genomic = converter.c2chrom('NM_012459.2:c.10_11insATC')
+ assert_equal(genomic, 'NC_000011.9:g.111957482_111957483insGAT')
+
+ def test_ins_seq_seq_c2chrom_reverse(self):
+ """
+ Insertion of two sequences on reverse strand (c2chrom).
+ """
+ converter = self._converter('hg19')
+ genomic = converter.c2chrom('NM_012459.2:c.10_11ins[TTT;ATC]')
+ assert_equal(genomic, 'NC_000011.9:g.111957482_111957483ins[GAT;AAA]')
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 7049fc3fa1a93ec03f5377021b575857a1e81e5d..4f4351585aaee48120032f63090ade94f83887e4 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -65,6 +65,21 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
+ @fix(cache('AL449423.14'))
+ def test_insertion_list_in_frame(self):
+ """
+ Simple in-frame insertion of a list should give a simple description
+ on protein level.
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.161_162ins[ATC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.61938_61939insGAT')
+ assert 'AL449423.14(CDKN2A_v001):c.161_162insATC' \
+ in self.output.getOutput('descriptions')
+ assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsIleSer)' \
+ in self.output.getOutput('protDescriptions')
+ assert self.output.getOutput('newprotein')
+
@fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame(self):
"""
@@ -81,6 +96,22 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
+ @fix(cache('AL449423.14'))
+ def test_deletion_insertion_list_in_frame(self):
+ """
+ Simple in-frame deletion-insertion of a list should give a simple
+ description on protein level.
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.161_162delins[ATCCC]',
+ self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.61938_61939delinsGGGAT')
+ assert 'AL449423.14(CDKN2A_v001):c.161_162delinsATCCC' \
+ in self.output.getOutput('descriptions')
+ assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
+ in self.output.getOutput('protDescriptions')
+ assert self.output.getOutput('newprotein')
+
@fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame_complete(self):
"""
@@ -97,6 +128,23 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('protDescriptions')
assert self.output.getOutput('newprotein')
+ @fix(cache('AL449423.14'))
+ def test_deletion_insertion_list_in_frame_complete(self):
+ """
+ Simple in-frame deletion-insertion of a list should give a simple
+ description on protein level, also with the optional deleted sequence
+ argument.
+ """
+ check_variant('AL449423.14(CDKN2A_v001):c.161_162delTGins[ATCCC]',
+ self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'AL449423.14:g.61938_61939delinsGGGAT')
+ assert 'AL449423.14(CDKN2A_v001):c.161_162delinsATCCC' \
+ in self.output.getOutput('descriptions')
+ assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
+ in self.output.getOutput('protDescriptions')
+ assert self.output.getOutput('newprotein')
+
@fix(cache('NM_003002.2'))
def test_est_warning_nm_est(self):
"""
@@ -496,20 +544,318 @@ class TestVariantchecker(MutalyzerTest):
# prediction is done.
assert self.output.getOutput('newprotein')
- @fix(cache('AB026906.1'))
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq(self):
+ """
+ Insertion of a sequence.
+ """
+ check_variant('NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+
+ @fix(cache('NG_012337.1'))
+ def test_ins_seq_reverse(self):
+ """
+ Insertion of a sequence on reverse strand.
+ """
+ check_variant('NG_012337.1(TIMM8B_v001):c.12_13insGATC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_012337.1:g.4911_4912insATCG')
+ assert 'NG_012337.1(TIMM8B_v001):c.12_13insGATC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
def test_ins_range(self):
"""
- Insertion of a range is not implemented yet.
+ Insertion of a range.
"""
- check_variant('AB026906.1:c.274_275ins262_268', self.output)
+ check_variant('NG_008939.1:g.5207_5208ins4300_4320', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_list(self):
+ """
+ Insertion of a sequence as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[GTCCTGTGCTCATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_012337.1'))
+ def test_ins_seq_list_reverse(self):
+ """
+ Insertion of a sequence as a list on reverse strand.
+ """
+ check_variant('NG_012337.1(TIMM8B_v001):c.12_13ins[GATC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_012337.1:g.4911_4912insATCG')
+ assert 'NG_012337.1(TIMM8B_v001):c.12_13insGATC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_list(self):
+ """
+ Insertion of a range as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_seq(self):
+ """
+ Insertion of two sequences.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[GTCCTGTGCTC;ATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_012337.1'))
+ def test_ins_seq_seq_reverse(self):
+ """
+ Insertion of two sequences on reverse strand.
+ """
+ check_variant('NG_012337.1(TIMM8B_v001):c.12_13ins[TTT;GATC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_012337.1:g.4911_4912insATCAAAG')
+ assert 'NG_012337.1(TIMM8B_v001):c.12_13insTTTGATC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_range(self):
+ """
+ Insertion of two ranges.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4309;4310_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_range(self):
+ """
+ Insertion of a sequence and a range.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[GTCCTGTGCT;4310_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_seq(self):
+ """
+ Insertion of a range and a sequence.
+ """
+ check_variant('NG_008939.1:g.5207_5208ins[4300_4309;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_coding(self):
+ """
+ Insertion of a sequence (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_list_coding(self):
+ """
+ Insertion of a sequence as a list (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157ins[GTCCTGTGCTCATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_seq_seq_coding(self):
+ """
+ Insertion of two sequences (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157ins[GTCCTGTGCTC;ATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5208insGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_157insGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_coding(self):
+ """
+ Insertion of a range (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_157ins180_188', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
- @fix(cache('AB026906.1'))
+ @fix(cache('NG_008939.1'))
+ def test_ins_range_list_coding(self):
+ """
+ Insertion of a range as a list (coding).
+ """
+ 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_delins_seq(self):
+ """
+ Insertion-deletion of a sequence.
+ """
+ check_variant('NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
def test_delins_range(self):
"""
- Deletion/insertion of a range is not implemented yet.
+ Insertion-deletion of a range.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins4300_4320', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_list(self):
+ """
+ Insertion-deletion of a sequence as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[GTCCTGTGCTCATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_list(self):
+ """
+ Insertion-deletion of a range as a list.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_seq(self):
+ """
+ Insertion-deletion of two sequences.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[GTCCTGTGCT;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_range(self):
+ """
+ Insertion-deletion of two ranges.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4309;4310_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+ assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 0)
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_range(self):
+ """
+ Insertion-deletion of a sequence and a range.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[GTCCTGTGCT;4310_4320]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_seq(self):
+ """
+ Insertion-deletion of a range and a sequence.
+ """
+ check_variant('NG_008939.1:g.5207_5212delins[4300_4309;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_coding(self):
+ """
+ Insertion-deletion of a sequence (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_list_coding(self):
+ """
+ Insertion-deletion of a sequence as a list (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delins[GTCCTGTGCTCATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_seq_seq_coding(self):
+ """
+ Insertion-deletion of two sequences (coding).
+ """
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delins[GTCCTGTGCT;CATTATCTGGC]', self.output)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NG_008939.1:g.5207_5212delinsGTCCTGTGCTCATTATCTGGC')
+ assert 'NG_008939.1(PCCB_v001):c.156_161delinsGTCCTGTGCTCATTATCTGGC' \
+ in self.output.getOutput('descriptions')
+
+ @fix(cache('NG_008939.1'))
+ def test_delins_range_coding(self):
+ """
+ Insertion-deletion of a range (coding).
+ """
+ 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_list_coding(self):
+ """
+ Insertion-deletion of a range as a list (coding).
"""
- check_variant('AB026906.1:c.274delins262_268', self.output)
+ check_variant('NG_008939.1(PCCB_v001):c.156_161delins[180_188]', self.output)
assert_equal(len(self.output.getMessagesWithErrorCode('ENOTIMPLEMENTED')), 1)
def test_no_reference(self):