def test_preserves_multiple_annotations(self):
replaced = self.middle[0:10]+self.middle[11:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(len(self.upstream)+2, len(self.upstream)+10, 'Bar', 'static', -1)
self.fragment.annotate(len(self.upstream)+len(self.front_bs)+1,
len(self.upstream)+len(self.front_bs)+len(self.middle),
'Foo', 'changed', 1)
r = find_swap_region_with_annotations(self.genome, cassette, self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 2)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], 2)
self.assertEquals(a['base_last'], 10)
self.assertEquals(a['feature_name'], 'Bar')
self.assertEquals(a['feature_type'], 'static')
self.assertEquals(a['feature_strand'], -1)
a = r[0].cassette_annotations[1]
self.assertEquals(a['base_first'], len(self.front_bs)+1)
self.assertEquals(a['base_last'], len(self.front_bs)+len(self.middle)-1)
self.assertEquals(a['feature_name'], 'Foo -11A')
self.assertEquals(a['feature_type'], 'changed')
self.assertEquals(a['feature_strand'], 1)
def test_preserves_multiple_annotations(self):
replaced = self.middle[0:13] + self.middle[14:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + 2,
len(self.upstream) + 10, 'Bar', 'static', -1)
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 1,
len(self.upstream) + len(self.front_bs) + len(self.middle), 'Foo',
'changed', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 2)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], 2)
self.assertEquals(a['base_last'], 10)
self.assertEquals(a['feature_name'], 'Bar')
self.assertEquals(a['feature_type'], 'static')
self.assertEquals(a['feature_strand'], -1)
a = r[0].cassette_annotations[1]
self.assertEquals(a['base_first'], len(self.front_bs) + 1)
self.assertEquals(a['base_last'],
len(self.front_bs) + len(self.middle) - 1)
self.assertEquals(a['feature_name'], 'Foo -14G')
self.assertEquals(a['feature_type'], 'changed')
self.assertEquals(a['feature_strand'], 1)
def test_does_not_preserve_annotation_if_replaced_is_different(self):
replaced = "aaaaaaaaaaaaaaaaaaa"
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(len(self.upstream)+len(self.front_bs),
len(self.upstream)+len(self.front_bs)+len(self.middle)-1,
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette, self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 0)
def test_does_not_preserve_annotation_if_replaced_is_different(self):
replaced = "aaaaaaaaaaaaaaaaaaa"
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs),
len(self.upstream) + len(self.front_bs) + len(self.middle) - 1,
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 0)
def test_detects_deletion(self):
replaced = self.middle[0:10]+self.middle[11:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(len(self.upstream)+len(self.front_bs)+1,
len(self.upstream)+len(self.front_bs)+len(self.middle),
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette, self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs)+1)
self.assertEquals(a['base_last'], len(self.front_bs)+len(self.middle)-1)
self.assertEquals(a['feature_name'], 'Foo -11A')
def test_preserves_annotation_with_single_mutation(self):
replaced = [c for c in self.middle]
self.assertEquals(replaced[10], 'a')
replaced[10] = 'c'
replaced = ''.join(replaced)
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(len(self.upstream)+len(self.front_bs)+1,
len(self.upstream)+len(self.front_bs)+len(self.middle),
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette, self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs)+1)
self.assertEquals(a['base_last'], len(self.front_bs)+len(self.middle))
self.assertEquals(a['feature_name'], 'Foo A11C')
def test_returns_new_orf(self):
replaced = 'atgatcatcatcatcatcatcatcatcatcatcatcatcatcatcatctag'
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(len(self.upstream)+len(self.front_bs)+1,
len(self.upstream)+len(self.front_bs)+len(self.middle),
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette, self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs)+1)
self.assertEquals(a['base_last'], len(self.front_bs)+len(replaced))
self.assertEquals(a['feature_name'], 'ORF frame 1')
self.assertEquals(a['feature_type'], 'ORF')
self.assertEquals(a['feature_strand'], 1)
def test_preserves_unchanged_annotation(self):
replaced = self.middle[0:10] + self.middle[11:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 12,
len(self.upstream) + len(self.front_bs) + len(self.middle) - 1,
'Foo', 'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs) + 12 - 1)
self.assertEquals(a['base_last'],
len(self.front_bs) + len(self.middle) - 1 - 1)
self.assertEquals(a['feature_name'], 'Foo')
def test_detects_deletion(self):
replaced = self.middle[0:13] + self.middle[14:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 1,
len(self.upstream) + len(self.front_bs) + len(self.middle), 'Foo',
'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs) + 1)
self.assertEquals(a['base_last'],
len(self.front_bs) + len(self.middle) - 1)
self.assertEquals(a['feature_name'], 'Foo -14G')
def test_returns_new_orf(self):
replaced = 'atgatcatcatcatcatcatcatcatcatcatcatcatcatcatcatctag'
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 1,
len(self.upstream) + len(self.front_bs) + len(self.middle), 'Foo',
'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs) + 1)
self.assertEquals(a['base_last'], len(self.front_bs) + len(replaced))
self.assertEquals(a['feature_name'], 'ORF frame 1')
self.assertEquals(a['feature_type'], 'ORF')
self.assertEquals(a['feature_strand'], 1)
def test_preserves_feature_direction_and_type(self):
replaced = self.middle[0:10] + self.middle[11:]
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 1,
len(self.upstream) + len(self.front_bs) + len(self.middle), 'Foo',
'foobar', -1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs) + 1)
self.assertEquals(a['base_last'],
len(self.front_bs) + len(self.middle) - 1)
self.assertEquals(a['feature_name'], 'Foo -11A')
self.assertEquals(a['feature_type'], 'foobar')
self.assertEquals(a['feature_strand'], -1)
def test_preserves_annotation_with_single_mutation(self):
replaced = [c for c in self.middle]
self.assertEquals(replaced[10], 'a')
replaced[10] = 'c'
replaced = ''.join(replaced)
cassette = ''.join([self.front_bs, replaced, self.back_bs])
self.fragment.annotate(
len(self.upstream) + len(self.front_bs) + 1,
len(self.upstream) + len(self.front_bs) + len(self.middle), 'Foo',
'gene', 1)
r = find_swap_region_with_annotations(self.genome, cassette,
self.arm_len)
self.assertEquals(len(r), 1)
self.assertEquals(len(r[0].cassette_annotations), 1)
a = r[0].cassette_annotations[0]
self.assertEquals(a['base_first'], len(self.front_bs) + 1)
self.assertEquals(a['base_last'],
len(self.front_bs) + len(self.middle))
self.assertEquals(a['feature_name'], 'Foo A11C')