def test_get_all_variants(self):
'''Test load all variants from file'''
deletion_snps = [
'\t'.join([
'125', 'T', '.', '124', '1', '124', '500', '497', '1', '1',
'ref1', 'qry1'
]),
'\t'.join([
'126', 'A', '.', '124', '1', '124', '500', '497', '1', '1',
'ref1', 'qry1'
]),
'\t'.join([
'127', 'C', '.', '124', '1', '124', '500', '497', '1', '1',
'ref1', 'qry1'
]),
]
deletion_snps = [snp.Snp(x) for x in deletion_snps]
deletion_variant = variant.Variant(deletion_snps[0])
deletion_variant.update_indel(deletion_snps[1])
deletion_variant.update_indel(deletion_snps[2])
just_a_snp = '\t'.join([
'386', 'C', 'T', '383', '115', '115', '500', '497', '1', '1',
'ref1', 'qry1'
])
snp_variant = variant.Variant(snp.Snp(just_a_snp))
insertion_snps = [
'\t'.join([
'479', '.', 'G', '480', '0', '22', '500', '504', '1', '1',
'ref2', 'qry2'
]),
'\t'.join([
'479', '.', 'A', '481', '0', '22', '500', '504', '1', '1',
'ref2', 'qry2'
]),
'\t'.join([
'479', '.', 'T', '482', '0', '22', '500', '504', '1', '1',
'ref2', 'qry2'
]),
'\t'.join([
'479', '.', 'A', '483', '0', '22', '500', '504', '1', '1',
'ref2', 'qry2'
]),
]
insertion_snps = [snp.Snp(x) for x in insertion_snps]
insertion_variant = variant.Variant(insertion_snps[0])
for i in range(1, len(insertion_snps)):
insertion_variant.update_indel(insertion_snps[i])
variants_from_file = snp_file.get_all_variants(
os.path.join(data_dir, 'snp_file_test_get_all_variants.snps'))
self.assertEqual(len(variants_from_file), 3)
self.assertEqual(variants_from_file[0], deletion_variant)
self.assertEqual(variants_from_file[1], snp_variant)
self.assertEqual(variants_from_file[2], insertion_variant)
def test_qry_coords_from_ref_coord_test_different_strand(self):
'''Test qry_coords_from_ref_coord on different strand'''
aln = alignment.Alignment('\t'.join(['100', '200', '101', '1', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry']))
snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # snp
snp0 = variant.Variant(snp0)
snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry
snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry
del1 = variant.Variant(snp1)
del2 = variant.Variant(snp1)
self.assertTrue(del2.update_indel(snp2))
snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
ins1 = variant.Variant(snp3)
ins2 = variant.Variant(snp3)
self.assertTrue(ins2.update_indel(snp4))
self.assertTrue(ins2.update_indel(snp5))
tests = [
(99, [], (100, False)),
(100, [], (99, False)),
(199, [], (0, False)),
(119, [], (80, False)),
(119, [del1], (80, False)),
(149, [], (50, False)),
(149, [del1], (51, False)),
(149, [del2], (52, False)),
(159, [], (40, False)),
(159, [ins1], (39, False)),
(159, [ins2], (37, False)),
(159, [del1, ins1], (40, False)),
(159, [del1, ins2], (38, False)),
(159, [del2, ins1], (41, False)),
(159, [del2, ins2], (39, False)),
(139, [del1], (39, True)),
(139, [snp0], (60, False)),
(149, [ins1], (49, True)),
]
for ref_coord, variant_list, expected in tests:
got = aln.qry_coords_from_ref_coord(ref_coord, variant_list)
self.assertEqual(expected, got)
# if we reverse the direction of hit in query and reference, should get the same answer
aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start
aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start
got = aln.qry_coords_from_ref_coord(ref_coord, variant_list)
self.assertEqual(expected, got)
aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start
aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start
def test_update_indel_deletion(self):
'''Test update_indel extends deletions correctly'''
deletion = variant.Variant(
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])))
to_add = snp.Snp('\t'.join([
'43', 'C', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
]))
expected = copy.copy(deletion)
# coords stored zero-based, so subtract 1 from the real expected coords
expected.ref_start = 41
expected.ref_end = 42
expected.ref_length = 300
expected.ref_name = 'ref'
expected.ref_base = 'AC'
expected.qry_start = 99
expected.qry_end = 99
expected.qry_length = 400
expected.qry_name = 'qry'
expected.qry_base = '.'
self.assertTrue(deletion.update_indel(to_add))
self.assertEqual(expected, deletion)
def get_all_variants(fname):
variants = []
fr = reader(fname)
for nucmer_snp in fr:
if len(variants) == 0 or not variants[-1].update_indel(nucmer_snp):
variants.append(variant.Variant(nucmer_snp))
return variants
def test_ref_coords_from_qry_coord_when_variant_not_in_nucmer_match(self):
'''Test ref_coords_from_qry_coord when variant not in nucmer match'''
aln = alignment.Alignment('1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry')
snp0 = snp.Snp('127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry')
indel = variant.Variant(snp0)
self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, []))
self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [indel]))
self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, []))
self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [indel]))
self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, []))
self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [indel]))
def test_intersects_variant(self):
'Test intersects_variant'''
snp0 = snp.Snp('100\tA\t.\t600\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry') #100 in ref, 600 in qry
indel = variant.Variant(snp0)
aln1 = alignment.Alignment('100\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln2 = alignment.Alignment('101\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln3 = alignment.Alignment('100\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln4 = alignment.Alignment('101\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
self.assertTrue(aln1.intersects_variant(indel))
self.assertFalse(aln2.intersects_variant(indel))
self.assertFalse(aln3.intersects_variant(indel))
self.assertFalse(aln4.intersects_variant(indel))
def test_init(self):
'''Test init gets correct variant type'''
lines = [[
'42', 'T', 'A', '42', '42', '42', '1000', '1000', '1', '1', 'ref',
'ref'
],
[
'242', 'G', '.', '241', '1', '241', '1000', '1000', '1',
'1', 'ref', 'ref'
],
[
'300', '.', 'G', '298', '0', '298', '1000', '1000', '1',
'1', 'ref', 'ref'
]]
variants = [variant.Variant(snp.Snp('\t'.join(x))) for x in lines]
expected = [variant.SNP, variant.DEL, variant.INS]
for i in range(len(lines)):
self.assertEqual(variants[i].var_type, expected[i])
def test_update_indel_no_change(self):
'''Test update_indel does nothing in the right cases'''
initial_vars = [
snp.Snp('\t'.join([
'42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
]
to_add = [
snp.Snp('\t'.join([
'142', 'A', '.', '1000', 'x', 'x', '2000', '3000', 'x', 'x',
'ref', 'qry'
])),
snp.Snp('\t'.join([
'142', '.', 'A', '1000', 'x', 'x', '2000', '3000', 'x', 'x',
'ref', 'qry'
])),
snp.Snp('\t'.join([
'43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x',
'ref2', 'qry'
])),
snp.Snp('\t'.join([
'43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry2'
])),
snp.Snp('\t'.join([
'44', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x',
'ref2', 'qry'
])),
snp.Snp('\t'.join([
'43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry2'
])),
snp.Snp('\t'.join([
'44', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
snp.Snp('\t'.join([
'42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', 'x', 'ref',
'qry'
])),
]
assert len(initial_vars) == len(to_add)
for i in range(len(initial_vars)):
var = variant.Variant(initial_vars[i])
var_original = copy.copy(var)
self.assertFalse(var.update_indel(to_add[i]))
self.assertEqual(var, var_original)