def test_order_of_genotypes(self):
run_id = self.no_chr_run['id']
query = {
'range': {},
'filters': [{'columnName': 'sample_name', 'filterValue': 'normal', 'type': '='}],
'sortBy': [{'columnName': 'contig', 'order': 'asc'},
{'columnName': 'position', 'order': 'asc'}]
}
records = genotypes.get(run_id, query, with_stats=False)['records']
results = [pick(r, 'contig', 'position') for r in records]
expected_results = [{'contig': '1', 'position': 1},
{'contig': '1', 'position': 2},
{'contig': '1', 'position': 10},
{'contig': '1', 'position': 11},
{'contig': '1', 'position': 21},
{'contig': '2', 'position': 1},
{'contig': '10', 'position': 17},
{'contig': '11', 'position': 163},
{'contig': '20', 'position': 123},
{'contig': '23', 'position': 1},
{'contig': 'X', 'position': 2},
{'contig': 'Y', 'position': 1},
{'contig': 'Y', 'position': 7},
{'contig': 'Y', 'position': 17},
{'contig': 'Y', 'position': 19},
{'contig': 'Y', 'position': 21},
{'contig': 'GTR01', 'position': 20},
{'contig': 'GT05182', 'position': 1}]
asserts.eq_(results, expected_results)
def test_order_of_genotypes_by_dp_asc(self):
run_id = self.no_chr_run['id']
query = {
'range': {},
'filters': [{'columnName': 'sample_name', 'filterValue': 'normal', 'type': '='}],
'sortBy': [{'columnName': 'sample:DP', 'order': 'asc'}]
}
records = genotypes.get(run_id, query, with_stats=False)['records']
results = [pick(r, 'contig', 'position', 'sample:DP') for r in records]
expected_results = [{'contig': 'Y', 'position': 21, 'sample:DP': '10'},
{'contig': 'Y', 'position': 1, 'sample:DP': '11'},
{'contig': 'Y', 'position': 7, 'sample:DP': '12'},
{'contig': 'Y', 'position': 19, 'sample:DP': '13'},
{'contig': 'Y', 'position': 17, 'sample:DP': '21'},
{'contig': '10', 'position': 17, 'sample:DP': '30'},
{'contig': '11', 'position': 163, 'sample:DP': '30'},
{'contig': '20', 'position': 123, 'sample:DP': '30'},
{'contig': 'X', 'position': 2, 'sample:DP': '32'},
{'contig': '2', 'position': 1, 'sample:DP': '45'},
{'contig': 'GTR01', 'position': 20, 'sample:DP': '45'},
{'contig': '1', 'position': 1, 'sample:DP': '67'},
{'contig': '1', 'position': 2, 'sample:DP': '67'},
{'contig': '1', 'position': 10, 'sample:DP': '67'},
{'contig': '1', 'position': 11, 'sample:DP': '67'},
{'contig': '1', 'position': 21, 'sample:DP': '67'},
{'contig': '23', 'position': 1, 'sample:DP': '99'},
{'contig': 'GT05182', 'position': 1, 'sample:DP': '99'}]
asserts.eq_(results, expected_results)
def test_filtered_sample_gt(self):
run_id = self.no_chr_run['id']
query = {
'range': {},
'filters': [{'columnName': 'sample:RD', 'filterValue': '35', 'type': '>'}],
'sortBy': []
}
records = genotypes.get(run_id, query, with_stats=False)['records']
results = [pick(r, 'contig', 'sample:RD', 'sample_name') for r in records]
expected_results = [{'contig': '1', 'sample:RD': '38', 'sample_name': 'normal'},
{'contig': '1', 'sample:RD': '36', 'sample_name': 'normal'},
{'contig': '1', 'sample:RD': '45', 'sample_name': 'normal'},
{'contig': '10', 'sample:RD': '72', 'sample_name': 'tumor'},
{'contig': 'Y', 'sample:RD': '67', 'sample_name': 'normal'},
{'contig': 'GTR01', 'sample:RD': '51', 'sample_name': 'tumor'},
{'contig': 'GT05182', 'sample:RD': '91', 'sample_name': 'normal'}]
asserts.eq_(len(results), 7)
asserts.eq_(results, expected_results)
def test_filtered_info_lt(self):
run_id = self.no_chr_run['id']
query = {
'range': {},
'filters': [{'columnName': 'sample_name', 'filterValue': 'tumor', 'type': '='},
{'columnName': 'info:DP', 'filterValue': '50', 'type': '<'}],
'sortBy': []
}
records = genotypes.get(run_id, query, with_stats=False)['records']
results = [pick(r, 'contig', 'position', 'info:DP') for r in records]
expected_results = [{'contig': '1', 'info:DP': '43', 'position': 11},
{'contig': '10', 'info:DP': '18', 'position': 17},
{'contig': '11', 'info:DP': '12', 'position': 163},
{'contig': '20', 'info:DP': '12', 'position': 123},
{'contig': 'Y', 'info:DP': '49', 'position': 1},
{'contig': 'GTR01', 'info:DP': '45', 'position': 20}]
asserts.eq_(len(results), 6)
asserts.eq_(results, expected_results)
def test_pick():
asserts.eq_(pick({'a': 1, 'b': 2, 'c': 'abc'}, 'a', 'c'), {'a': 1, 'c': 'abc'})
asserts.eq_(pick({'a': 1, 'b': 2, 'c': 'abc'}), {})
pick({'a': 'oh no'}, 'b') # This raises a KeyError