def table_irs(self):
b = ir.TrueIR()
table_read = ir.TableRead(
'src/test/resources/backward_compatability/1.0.0/table/0.ht',
False, None)
table_read_row_type = hl.dtype(
'struct{idx: int32, f32: float32, i64: int64, m: float64, astruct: struct{a: int32, b: float64}, mstruct: struct{x: int32, y: str}, aset: set<str>, mset: set<float64>, d: dict<array<str>, float64>, md: dict<int32, str>, h38: locus<GRCh38>, ml: locus<GRCh37>, i: interval<locus<GRCh37>>, c: call, mc: call, t: tuple(call, str, str), mt: tuple(locus<GRCh37>, bool)}'
)
matrix_read = ir.MatrixRead(
'src/test/resources/backward_compatability/1.0.0/matrix_table/0.hmt',
False, False)
range = ir.TableRange(10, 4)
table_irs = [
ir.TableUnkey(table_read),
ir.TableKeyBy(table_read, ['m', 'd'], 1, True),
ir.TableFilter(table_read, b), table_read,
ir.MatrixColsTable(matrix_read),
ir.TableAggregateByKey(table_read,
ir.MakeStruct([('a', ir.I32(5))])),
ir.TableKeyByAndAggregate(table_read,
ir.MakeStruct([('a', ir.I32(5))]),
ir.MakeStruct([('b', ir.I32(5))]), 1, 2),
ir.TableJoin(table_read, ir.TableRange(100, 10), 'inner'),
ir.MatrixEntriesTable(matrix_read),
ir.MatrixRowsTable(matrix_read),
ir.TableParallelize(
'Table{global:Struct{},key:None,row:Struct{a:Int32}}',
ir.Value(hl.tarray(hl.tstruct(a=hl.tint32)), [{
'a': None
}, {
'a': 5
}, {
'a': -3
}]), None),
ir.TableMapRows(
table_read,
ir.MakeStruct([('a',
ir.GetField(ir.Ref('row', table_read_row_type),
'f32')), ('b', ir.F64(-2.11))]),
None, None),
ir.TableMapGlobals(
table_read,
ir.MakeStruct([('foo', ir.NA(hl.tarray(hl.tint32)))]),
ir.Value(hl.tstruct(), {})),
ir.TableRange(100, 10),
ir.TableRepartition(table_read, 10, False),
ir.TableUnion([ir.TableRange(100, 10),
ir.TableRange(50, 10)]),
ir.TableExplode(table_read, 'mset'),
ir.TableHead(table_read, 10),
ir.TableOrderBy(ir.TableUnkey(table_read), [('m', 'A'),
('m', 'D')]),
ir.TableDistinct(table_read),
ir.LocalizeEntries(matrix_read, '__entries')
]
return table_irs
def test_matrix_ir_parses(self):
hl.index_bgen(resource('example.8bits.bgen'),
reference_genome=hail.get_reference('GRCh37'),
contig_recoding={'01': '1'})
collect_sig = ir.AggSignature('Collect', [], None, [hl.tint32])
collect = ir.MakeStruct([('x',
ir.ApplyAggOp([ir.I32(0)], [], None,
collect_sig,
hl.tarray(hl.tint32)))])
matrix_read = ir.MatrixRead(
resource('backward_compatability/1.0.0/matrix_table/0.hmt'), False,
False)
table_read = ir.TableRead(
resource('backward_compatability/1.0.0/table/0.ht'), False, None)
matrix_irs = [
ir.MatrixUnionRows(ir.MatrixRange(5, 5, 1),
ir.MatrixRange(5, 5, 1)),
ir.UnlocalizeEntries(ir.LocalizeEntries(matrix_read, '__entries'),
ir.MatrixColsTable(matrix_read), '__entries'),
ir.MatrixAggregateRowsByKey(matrix_read, collect, collect),
ir.MatrixAggregateColsByKey(matrix_read, collect, collect),
ir.MatrixRange(1, 1, 10),
ir.MatrixImportVCF([resource('sample.vcf')], False, False,
None, None, False, ['GT'],
hail.get_reference('GRCh37'), {}, True, False),
ir.MatrixImportBGEN([resource('example.8bits.bgen')], ['GP'],
resource('example.sample'), {}, 10, 1,
['varid'], None),
ir.MatrixFilterRows(matrix_read, ir.FalseIR()),
ir.MatrixFilterCols(matrix_read, ir.FalseIR()),
ir.MatrixFilterEntries(matrix_read, ir.FalseIR()),
ir.MatrixChooseCols(matrix_read, [1, 0]),
ir.MatrixMapCols(matrix_read, ir.MakeStruct([('x', ir.I64(20))]),
['x']),
ir.MatrixKeyRowsBy(matrix_read, ['row_i64'], False),
ir.MatrixMapRows(ir.MatrixKeyRowsBy(matrix_read, []),
ir.MakeStruct([('x', ir.I64(20))])),
ir.MatrixMapEntries(matrix_read,
ir.MakeStruct([('x', ir.I64(20))])),
ir.MatrixMapGlobals(matrix_read,
ir.MakeStruct([('x', ir.I64(20))])),
ir.TableToMatrixTable(table_read, ['f32', 'i64'], ['m', 'astruct'],
['aset'], ['mset'], 100),
ir.MatrixCollectColsByKey(matrix_read),
ir.MatrixExplodeRows(matrix_read, ['row_aset']),
ir.MatrixExplodeCols(matrix_read, ['col_aset']),
ir.MatrixAnnotateRowsTable(matrix_read, table_read, '__foo', None),
ir.MatrixAnnotateColsTable(matrix_read, table_read, '__foo'),
]
for x in matrix_irs:
try:
Env.hail().expr.Parser.parse_matrix_ir(str(x))
except Exception as e:
raise ValueError(str(x)) from e