def test_change_chroms_mismatch(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 118, "T", "C", 118)
variant2 = veffects.VariantRecord("3L", 118, "T", "C", 118)
variants = [variant1, variant2]
self.assertRaises(ValueError, self.exon.add_sequence, variants)
def test_overlapping_variant_error(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 117, "AT", "A", 118)
variant2 = veffects.VariantRecord("2L", 115, "GAATA", "G", 119)
variants = [variant1, variant2]
self.exon.variants = variants
self.assertRaises(veffects.OverlappingVariantError, self.exon.change)
def test_multi_base_ref_alelle(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 118, "TA", "AA", 119)
variant2 = veffects.VariantRecord("2L", 127, "ATA", "CTA", 129)
variants = [variant1, variant2]
self.exon.variants = variants
self.exon.change()
test_changed_seq = "CGATATGAAAATGACCAGCTATGAGT"
self.assertEqual(self.exon.changed_sequence, test_changed_seq)
def test_change_allele_out_of_bounds(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 4, "G", "GGGG", 4)
self.assertRaises(ValueError, self.exon.add_sequence, [variant1])
def test_change_ref_alleles_mismatch(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 131, "GGG", "G", 133)
self.assertRaises(ValueError, self.exon.add_sequence, [variant1])
def test_change(self):
self.exon.add_sequence(self.test_seq)
variant1 = veffects.VariantRecord("2L", 110, "GA", "G", 111)
variant2 = veffects.VariantRecord("2L", 118, "T", "C", 118)
variant3 = veffects.VariantRecord("2L", 125, "A", "AAAAAAA", 125)
variant4 = veffects.VariantRecord("2L", 131, "GAG", "G", 133)
variants = [variant1, variant2, variant3, variant4]
self.exon.variants = variants
test_changed_seq = "CGTATGAACATGACCAAAAAAAGATATGT"
self.exon.change()
self.assertEqual(self.exon.changed_sequence, test_changed_seq)
def setUp(self):
test_seq = "ATGCTTCATCAGCAGCAGCCCGGGGCCTAG"
self.transcript = veffects.Transcript("2L", test_seq)
exon1 = veffects.ExonSequence("2L", "foo", 1, "+", 5, 18) #14
exon2 = veffects.ExonSequence("2L", "foo", 2, "+", 50, 55) #6
exon3 = veffects.ExonSequence("2L", "foo", 3, "+", 70, 74) #5
exon4 = veffects.ExonSequence("2L", "foo", 4, "+", 103, 107) #5
self.exons = [exon1, exon2, exon3, exon4]
variant1 = veffects.VariantRecord("2L", 15, "A", "AA", 15)
variant2 = veffects.VariantRecord("2L", 16, "GCA", "G", 18)
variant3 = veffects.VariantRecord("2L", 52, "A", "AAAAA", 52)
variant4 = veffects.VariantRecord("2L", 70, "CGG", "C", 72)
self.variants = [variant1, variant2, variant3, variant4]
def test_catches_overlapping_variants(self):
##pass a set of variants that overlaps an exon boundary
##and make sure a VariantOverlapsExonBoundaryError is raised
for exon in self.exons:
self.transcript.add_exon(exon)
variant5 = veffects.VariantRecord("2L", 4, "CAT", "C", 6)
self.assertRaises(veffects.VariantCrossesExonBoundaryError,
self.transcript.check_for_overlapping_variants,
[variant5])