diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index 91ddb1994c9cacd1506391ee476c65dbff00e34b..f4a8ad2a4b6c84ad10e3da5556a037b047f20934 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -645,11 +645,31 @@ class GenRecord() :
forwardStop = stop_g
reverseStart = stop_g
reverseStop = start_g
+
+ if self.record.orientation == 1:
+ chromStart = self.record.toChromPos(start_g)
+ chromStop = self.record.toChromPos(stop_g)
+ chromArg1 = arg1
+ chromArg2 = arg2
+ else:
+ chromStart = self.record.toChromPos(stop_g)
+ chromStop = self.record.toChromPos(start_g)
+ chromArg1 = Bio.Seq.reverse_complement(arg1)
+ chromArg2 = Bio.Seq.reverse_complement(arg2)
+ # Todo: Should we use arg1_reverse here?
+
if roll :
forwardStart += roll[1]
forwardStop += roll[1]
reverseStart -= roll[0]
reverseStop -= roll[0]
+ if chromStart is not None:
+ if self.record.orientation == 1:
+ chromStart += roll[1]
+ chromStop += roll[1]
+ else:
+ chromStart += roll[0]
+ chromStop += roll[0]
#if
if varType != "subst" :
@@ -675,14 +695,12 @@ class GenRecord() :
self.record.addToDescription("(%s_%s)%s%s" % (
forwardStart, forwardStop, varType, arg1))
self.record.addToChromDescription("(%s_%s)%s%s" % (
- self.record.toChromPos(forwardStart),
- self.record.toChromPos(forwardStop), varType, arg1))
+ chromStart, chromStop, varType, chromArg1))
else:
self.record.addToDescription("%s_%s%s%s" % (
forwardStart, forwardStop, varType, arg1))
self.record.addToChromDescription("%s_%s%s%s" % (
- self.record.toChromPos(forwardStart),
- self.record.toChromPos(forwardStop), varType, arg1))
+ chromStart, chromStop, varType, chromArg1))
#if
else :
if start_fuzzy or stop_fuzzy:
@@ -691,12 +709,12 @@ class GenRecord() :
self.record.addToDescription("(%s)%s%s" % (
forwardStart, varType, arg1))
self.record.addToChromDescription("(%s)%s%s" % (
- self.record.toChromPos(forwardStart), varType, arg1))
+ chromStart, varType, chromArg1))
else:
self.record.addToDescription("%s%s%s" % (
forwardStart, varType, arg1))
self.record.addToChromDescription("%s%s%s" % (
- self.record.toChromPos(forwardStart), varType, arg1))
+ chromStart, varType, chromArg1))
#else
#if
else :
@@ -706,12 +724,12 @@ class GenRecord() :
self.record.addToDescription("(%s)%c>%c" % (
forwardStart, arg1, arg2))
self.record.addToChromDescription("(%s)%c>%c" % (
- self.record.toChromPos(forwardStart), arg1, arg2))
+ chromStart, chromArg1, chromArg2))
else:
self.record.addToDescription("%s%c>%c" % (
forwardStart, arg1, arg2))
self.record.addToChromDescription("%s%c>%c" % (
- self.record.toChromPos(forwardStart), arg1, arg2))
+ chromStart, chromArg1, chromArg2))
for i in self.record.geneList :
for j in i.transcriptList :
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index a078ec890e0765e09633833e73337133791cc65d..11557bff1fb356e97e7c205012466d50a0b50c5d 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -528,6 +528,148 @@ class TestVariantchecker():
assert 'UD_127955523176(DMD_v001):c.=' \
in self.output.getOutput('descriptions')
+ @skip
+ def test_ud_reverse_sequence(self):
+ """
+ Variant on UD from reverse strand should have reverse complement
+ sequence.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_132680290559(DPYD_v1):c.85C>T', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000001.10:g.98348885G>A')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_132680290559:g.42731C>T')
+ assert 'UD_132680290559(DPYD_v001):c.85C>T' \
+ in self.output.getOutput('descriptions')
+
+ @skip
+ def test_ud_forward_sequence(self):
+ """
+ Variant on UD from forward strand should have forward sequence.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_132680514783(MARK1_v001):c.400T>C', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000001.10:g.220773181T>C')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_132680514783:g.76614T>C')
+ assert 'UD_132680514783(MARK1_v001):c.400T>C' \
+ in self.output.getOutput('descriptions')
+
+ @skip
+ def test_ud_reverse_range(self):
+ """
+ Variant on UD from reverse strand should have reversed range
+ positions.
+
+ This UD number is for DPYD.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_133130716532:g.10624_78132del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000009.11:g.32928508_32996016del')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_133130716532:g.10624_78132del')
+
+ @skip
+ def test_ud_forward_range(self):
+ """
+ Variant on UD from forward strand should have forward range positions.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_132680514783(MARK1_v001):c.400_415del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000001.10:g.220773181_220773196del')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_132680514783:g.76614_76629del')
+
+ @skip
+ def test_ud_reverse_del_length(self):
+ """
+ Variant on UD from reverse strand should have reversed range
+ positions, but not reverse complement of first argument (it is not a
+ sequence, but a length).
+
+ This UD number is for DPYD.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_133130716532:g.10624_78132del67509', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000009.11:g.32928508_32996016del')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_133130716532:g.10624_78132del')
+
+ @skip
+ def test_ud_reverse_roll(self):
+ """
+ Variant on UD from reverse strand should roll the oposite direction.
+
+ The situation is as follows:
+
+ G A A A T T
+ c. 102 103 104 105 106 107
+ g. 748 749 750 751 752 753
+ chr g. 868 867 866 865 864 863
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_132680290559(DPYD_v001):c.104del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000001.10:g.98348867del')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_132680290559:g.42751del')
+ assert 'UD_132680290559(DPYD_v001):c.105del' \
+ in self.output.getOutput('descriptions')
+
+ @skip
+ def test_ud_forward_roll(self):
+ """
+ Variant on UD from forward strand should roll the same.
+
+ The situation is as follows:
+
+ A T T T A
+ c. 398 399 400 401 402
+ g. 612 613 614 615 616
+ chr g. 179 180 181 182 183
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_132680514783(MARK1_v001):c.400del', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000001.10:g.220773182del')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_132680514783:g.76615del')
+ assert 'UD_132680514783(MARK1_v001):c.401del' \
+ in self.output.getOutput('descriptions')
+
def test_deletion_with_sequence_forward_genomic(self):
"""
Specify the deleted sequence in a deletion.