def split_MNP_variant(var, include_ref_calls=False):
if var.type != variant.TYPE_MNP:
yield var
else:
for index, (ref, alt) in enumerate(zip(var.ref, var.alt)):
if ref != alt or include_ref_calls:
yield variant.Variant(var.chrom, index + var.pos_from, ref, alt)
def test_variant_from_vcf(self):
chrom = "blah"
pos = 21
ref = "hell"
alt = "heaven"
self.assertEqual(variant_from_vcf(chrom, pos, ref, alt),
variant.Variant(chrom, 20, ref, alt))
def variant_from_vcf(chrom_column, pos_column, ref_column, alt_column):
return variant.Variant(
chrom_column,
from_vcf_str(
pos_column,
int) - 1,
ref_column,
alt_column)
def test_eq(self):
reference = variant.Variant("1", 10, "ACGT", "ACC")
self.assertEqual(reference, variant.Variant("1", 10, "ACGT", "ACC"))
self.assertNotEqual(reference, variant.Variant("2", 10, "ACGT", "ACC"))
self.assertNotEqual(reference, variant.Variant("1", 11, "ACGT", "ACC"))
self.assertNotEqual(reference, variant.Variant("1", 10, "ACGC", "ACC"))
self.assertNotEqual(reference, variant.Variant("1", 10, "ACGT", "ACT"))
def test_lt(self):
reference = variant.Variant("1", 10, "ACGT", "ACC")
self.assertFalse(reference < reference)
self.assertGreaterEqual(reference,
variant.Variant("1", 10, "ACGT", "ACC"))
self.assertLess(reference, variant.Variant("2", 10, "ACGT", "ACC"))
self.assertLess(reference, variant.Variant("1", 11, "ACGT", "ACC"))
self.assertLess(reference, variant.Variant("1", 10, "CCGT", "ACC"))
self.assertLess(reference, variant.Variant("1", 10, "ACGT", "ACT"))
def test_ne(self):
"""
Note: self.assert[Not]Equal() doesn't work in this case.
"""
reference = variant.Variant("1", 10, "ACGT", "ACC")
self.assertFalse(reference != variant.Variant("1", 10, "ACGT", "ACC"))
self.assertTrue(reference != variant.Variant("2", 10, "ACGT", "ACC"))
self.assertTrue(reference != variant.Variant("1", 11, "ACGT", "ACC"))
self.assertTrue(reference != variant.Variant("1", 10, "ACGC", "ACC"))
self.assertTrue(reference != variant.Variant("1", 10, "ACGT", "ACT"))
def test_split_MNP_variant(self):
chrom = "blah"
pos = 21
ref = "hell"
alt = "beli"
var = variant.Variant(chrom, pos, ref, alt)
self.assertEqual(list(split_MNP_variant(var)), [
variant.Variant(chrom, pos, ref[0], alt[0]),
variant.Variant(chrom, pos + 3, ref[3], alt[3]),
])
self.assertEqual(list(split_MNP_variant(var, include_ref_calls=True)),
[
variant.Variant(chrom, pos, ref[0], alt[0]),
variant.Variant(chrom, pos + 1, ref[1], alt[1]),
variant.Variant(chrom, pos + 2, ref[2], alt[2]),
variant.Variant(chrom, pos + 3, ref[3], alt[3]),
])
def with_variant(self, chrom, pos_from, ref, alt):
return self.with_record(
self.generate_record_from_variant(
variant.Variant(chrom, pos_from, ref, alt)))
def trim_variant(var):
start_offset, ref, alt = trimmed_vcf_ref_alt(var.ref, var.alt)
return variant.Variant(var.chrom, start_offset + var.pos_from, ref, alt)
def test_should_overlap_mnp_at_region_end(self):
mnp = variant.Variant('1', 15, 'ACGT', 'GCGC')
self.assertTrue(mnp.overlap(ChromInterval('1', 15, 16)))
def test_as_key(self):
variant_obj = variant.Variant("1", 10, "ACGT", "ACC")
expected_key = ("1", 10, 14, "ACGT", "ACC")
self.assertEqual(hash(expected_key), hash(variant_obj),
"Variant hash is broken.")
def test_should_not_overlap_mnp_after_region(self):
mnp = variant.Variant('1', 15, 'ACGT', 'GCGC')
self.assertFalse(mnp.overlap(ChromInterval('1', 19, 20)))
def test_should_overlap_deletion_at_region_end(self):
deletion = variant.Variant('1', 15, 'AAAAA', 'A')
self.assertTrue(deletion.overlap(ChromInterval('1', 15, 16)))
def test_should_not_overlap_insertion_before_region(self):
ins = variant.Variant('1', 15, 'A', 'AAAAA')
self.assertFalse(ins.overlap(ChromInterval('1', 16, 20)))
def test_should_overlap_insertion_at_region_end(self):
ins = variant.Variant('1', 15, 'A', 'AAAAA')
self.assertTrue(ins.overlap(ChromInterval('1', 15, 16)))
def test_should_not_overlap_deletion_after_region(self):
deletion = variant.Variant('1', 15, 'AAAAA', 'A')
self.assertFalse(deletion.overlap(ChromInterval('1', 20, 21)))
def test_variant_type(self):
chrom = "1"
pos_from = 100
self.assertEqual(
variant.Variant(chrom, pos_from, 'T', '.').type, variant.TYPE_REF)
self.assertEqual(
variant.Variant(chrom, pos_from, 'C', 'C').type, variant.TYPE_REF)
self.assertEqual(
variant.Variant(chrom, pos_from, 'CTC', 'CTC').type,
variant.TYPE_REF)
self.assertEqual(
variant.Variant(chrom, pos_from, 'T', 'TA').type, variant.TYPE_INS)
self.assertEqual(
variant.Variant(chrom, pos_from, 'CTG', 'CTAG').type,
variant.TYPE_INS)
self.assertEqual(
variant.Variant(chrom, pos_from, 'TA', 'A').type, variant.TYPE_DEL)
self.assertEqual(
variant.Variant(chrom, pos_from, 'AT', 'A').type, variant.TYPE_DEL)
self.assertEqual(
variant.Variant(chrom, pos_from, 'T', 'A').type, variant.TYPE_SNP)
self.assertEqual(
variant.Variant(chrom, pos_from, 'TGT', 'AGT').type,
variant.TYPE_SNP)
self.assertEqual(
variant.Variant(chrom, pos_from, 'TGTT', 'TGAT').type,
variant.TYPE_SNP)
self.assertEqual(
variant.Variant(chrom, pos_from, 'AGTT', 'TGAT').type,
variant.TYPE_MNP)
self.assertEqual(
variant.Variant(chrom, pos_from, 'AGTTATAT', 'TGATAAAT').type,
variant.TYPE_MNP)
self.assertEqual(
variant.Variant(chrom, pos_from, 'A', '<INS:ME_ALU>').type,
variant.TYPE_SYM)