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import unittest
import copy
import os
from pymummer import variant, snp
modules_dir = os.path.dirname(os.path.abspath(variant.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestVariant(unittest.TestCase):
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', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', 'C', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
]
to_add = [
snp.Snp('\t'.join(['142', 'A', '.', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['142', '.', 'A', '1000', 'x', 'x', '2000', '3000', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])),
snp.Snp('\t'.join(['43', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])),
snp.Snp('\t'.join(['44', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref2', 'qry'])),
snp.Snp('\t'.join(['43', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry2'])),
snp.Snp('\t'.join(['44', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '1', 'ref', 'qry'])),
snp.Snp('\t'.join(['42', 'A', '.', '100', 'x', 'x', '300', '400', 'x', '1', '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)
def test_update_indel_insertion(self):
'''Test update_indel extends insertions correctly'''
insertion = variant.Variant(snp.Snp('\t'.join(['42', '.', 'A', '100', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry'])))
to_add = snp.Snp('\t'.join(['42', '.', 'C', '101', 'x', 'x', '300', '400', 'x', '-1', 'ref', 'qry']))
expected = copy.copy(insertion)
# coords stored zero-based, so subtract 1 from the real expected coords
expected.ref_start = 41
expected.ref_end = 41
expected.ref_length = 300
expected.ref_name = 'ref'
expected.ref_base = '.'
expected.qry_start = 99
expected.qry_end = 100
expected.qry_length = 400
expected.qry_name = 'qry'
expected.qry_base = 'AC'
self.assertTrue(insertion.update_indel(to_add))
self.assertEqual(expected, insertion)
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', '1', 'ref', 'qry'])))
to_add = snp.Snp('\t'.join(['43', 'C', '.', '100', 'x', 'x', '300', '400', 'x', '1', '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)
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