# Copyright 2018 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Tests for vcf_parser module."""
from __future__ import absolute_import
import logging
import unittest
from itertools import permutations
from gcp_variant_transforms.beam_io import vcfio
from gcp_variant_transforms.beam_io.vcfio import Variant
from gcp_variant_transforms.beam_io.vcfio import VariantCall
from gcp_variant_transforms.testing.testdata_util import hash_name
class VariantTest(unittest.TestCase):
def _assert_variants_equal(self, actual, expected):
self.assertEqual(
sorted(expected),
sorted(actual))
def test_sort_variants(self):
sorted_variants = [
Variant(reference_name='a', start=20, end=22),
Variant(reference_name='a', start=20, end=22, quality=20),
Variant(reference_name='b', start=20, end=22),
Variant(reference_name='b', start=21, end=22),
Variant(reference_name='b', start=21, end=23)]
for permutation in permutations(sorted_variants):
self.assertEqual(sorted(permutation), sorted_variants)
def test_variant_equality(self):
base_variant = Variant(reference_name='a', start=20, end=22,
reference_bases='a', alternate_bases=['g', 't'],
names=['variant'], quality=9, filters=['q10'],
info={'key': 'value'},
calls=[VariantCall(genotype=[0, 0])])
equal_variant = Variant(reference_name='a', start=20, end=22,
reference_bases='a', alternate_bases=['g', 't'],
names=['variant'], quality=9, filters=['q10'],
info={'key': 'value'},
calls=[VariantCall(genotype=[0, 0])])
different_calls = Variant(reference_name='a', start=20, end=22,
reference_bases='a', alternate_bases=['g', 't'],
names=['variant'], quality=9, filters=['q10'],
info={'key': 'value'},
calls=[VariantCall(genotype=[1, 0])])
missing_field = Variant(reference_name='a', start=20, end=22,
reference_bases='a', alternate_bases=['g', 't'],
names=['variant'], quality=9, filters=['q10'],
info={'key': 'value'})
self.assertEqual(base_variant, equal_variant)
self.assertNotEqual(base_variant, different_calls)
self.assertNotEqual(base_variant, missing_field)
class VariantCallTest(unittest.TestCase):
def _default_variant_call(self):
return vcfio.VariantCall(
sample_id=hash_name('Sample1'), genotype=[1, 0],
phaseset=vcfio.DEFAULT_PHASESET_VALUE, info={'GQ': 48})
def test_variant_call_order(self):
variant_call_1 = self._default_variant_call()
variant_call_2 = self._default_variant_call()
self.assertEqual(variant_call_1, variant_call_2)
variant_call_1.phaseset = 0
variant_call_2.phaseset = 1
self.assertGreater(variant_call_2, variant_call_1)
if __name__ == '__main__':
logging.getLogger().setLevel(logging.INFO)
unittest.main()
