Esempio n. 1
0
    def test_aggregate2(self):
        schema = hl.tstruct(status=hl.tint32, GT=hl.tcall, qPheno=hl.tint32)

        rows = [{'status': 0, 'GT': hl.Call([0, 0]), 'qPheno': 3},
                {'status': 0, 'GT': hl.Call([0, 1]), 'qPheno': 13}]

        kt = hl.Table.parallelize(rows, schema)

        result = convert_struct_to_dict(
            kt.group_by(status=kt.status)
                .aggregate(
                x1=agg.collect(kt.qPheno * 2),
                x2=agg.explode(lambda elt: agg.collect(elt), [kt.qPheno, kt.qPheno + 1]),
                x3=agg.min(kt.qPheno),
                x4=agg.max(kt.qPheno),
                x5=agg.sum(kt.qPheno),
                x6=agg.product(hl.int64(kt.qPheno)),
                x7=agg.count(),
                x8=agg.count_where(kt.qPheno == 3),
                x9=agg.fraction(kt.qPheno == 1),
                x10=agg.stats(hl.float64(kt.qPheno)),
                x11=agg.hardy_weinberg_test(kt.GT),
                x13=agg.inbreeding(kt.GT, 0.1),
                x14=agg.call_stats(kt.GT, ["A", "T"]),
                x15=agg.collect(hl.Struct(a=5, b="foo", c=hl.Struct(banana='apple')))[0],
                x16=agg.collect(hl.Struct(a=5, b="foo", c=hl.Struct(banana='apple')).c.banana)[0],
                x17=agg.explode(lambda elt: agg.collect(elt), hl.null(hl.tarray(hl.tint32))),
                x18=agg.explode(lambda elt: agg.collect(elt), hl.null(hl.tset(hl.tint32))),
                x19=agg.take(kt.GT, 1, ordering=-kt.qPheno)
            ).take(1)[0])

        expected = {u'status': 0,
                    u'x13': {u'n_called': 2, u'expected_homs': 1.64, u'f_stat': -1.777777777777777,
                             u'observed_homs': 1},
                    u'x14': {u'AC': [3, 1], u'AF': [0.75, 0.25], u'AN': 4, u'homozygote_count': [1, 0]},
                    u'x15': {u'a': 5, u'c': {u'banana': u'apple'}, u'b': u'foo'},
                    u'x10': {u'min': 3.0, u'max': 13.0, u'sum': 16.0, u'stdev': 5.0, u'n': 2, u'mean': 8.0},
                    u'x8': 1, u'x9': 0.0, u'x16': u'apple',
                    u'x11': {u'het_freq_hwe': 0.5, u'p_value': 0.5},
                    u'x2': [3, 4, 13, 14], u'x3': 3, u'x1': [6, 26], u'x6': 39, u'x7': 2, u'x4': 13, u'x5': 16,
                    u'x17': [],
                    u'x18': [],
                    u'x19': [hl.Call([0, 1])]}

        self.maxDiff = None

        self.assertDictEqual(result, expected)
Esempio n. 2
0
    def test_aggregate2(self):
        schema = hl.tstruct(status=hl.tint32, GT=hl.tcall, qPheno=hl.tint32)

        rows = [{'status': 0, 'GT': hl.Call([0, 0]), 'qPheno': 3},
                {'status': 0, 'GT': hl.Call([0, 1]), 'qPheno': 13}]

        kt = hl.Table.parallelize(rows, schema)

        result = convert_struct_to_dict(
            kt.group_by(status=kt.status)
                .aggregate(
                x1=agg.collect(kt.qPheno * 2),
                x2=agg.explode(lambda elt: agg.collect(elt), [kt.qPheno, kt.qPheno + 1]),
                x3=agg.min(kt.qPheno),
                x4=agg.max(kt.qPheno),
                x5=agg.sum(kt.qPheno),
                x6=agg.product(hl.int64(kt.qPheno)),
                x7=agg.count(),
                x8=agg.count_where(kt.qPheno == 3),
                x9=agg.fraction(kt.qPheno == 1),
                x10=agg.stats(hl.float64(kt.qPheno)),
                x11=agg.hardy_weinberg_test(kt.GT),
                x13=agg.inbreeding(kt.GT, 0.1),
                x14=agg.call_stats(kt.GT, ["A", "T"]),
                x15=agg.collect(hl.Struct(a=5, b="foo", c=hl.Struct(banana='apple')))[0],
                x16=agg.collect(hl.Struct(a=5, b="foo", c=hl.Struct(banana='apple')).c.banana)[0],
                x17=agg.explode(lambda elt: agg.collect(elt), hl.null(hl.tarray(hl.tint32))),
                x18=agg.explode(lambda elt: agg.collect(elt), hl.null(hl.tset(hl.tint32))),
                x19=agg.take(kt.GT, 1, ordering=-kt.qPheno)
            ).take(1)[0])

        expected = {u'status': 0,
                    u'x13': {u'n_called': 2, u'expected_homs': 1.64, u'f_stat': -1.777777777777777,
                             u'observed_homs': 1},
                    u'x14': {u'AC': [3, 1], u'AF': [0.75, 0.25], u'AN': 4, u'homozygote_count': [1, 0]},
                    u'x15': {u'a': 5, u'c': {u'banana': u'apple'}, u'b': u'foo'},
                    u'x10': {u'min': 3.0, u'max': 13.0, u'sum': 16.0, u'stdev': 5.0, u'n': 2, u'mean': 8.0},
                    u'x8': 1, u'x9': 0.0, u'x16': u'apple',
                    u'x11': {u'het_freq_hwe': 0.5, u'p_value': 0.5},
                    u'x2': [3, 4, 13, 14], u'x3': 3, u'x1': [6, 26], u'x6': 39, u'x7': 2, u'x4': 13, u'x5': 16,
                    u'x17': [],
                    u'x18': [],
                    u'x19': [hl.Call([0, 1])]}

        self.maxDiff = None

        self.assertDictEqual(result, expected)