def test_matrix_ir_parses(self):
matrix_irs = [
ir.MatrixUnionRows(ir.MatrixRange(5, 5, 1), ir.MatrixRange(5, 5, 1))
]
for x in matrix_irs:
Env.hail().expr.Parser.parse_matrix_ir(str(x))
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
def test_matrix_ir_parses(self):
hl.index_bgen(resource('example.8bits.bgen'),
reference_genome=hl.get_reference('GRCh37'),
contig_recoding={'01': '1'})
collect = ir.MakeStruct([('x', ir.ApplyAggOp('Collect', [], None, [ir.I32(0)]))])
matrix_read = ir.MatrixRead(
ir.MatrixNativeReader(resource('backward_compatability/1.0.0/matrix_table/0.hmt')), False, False)
table_read = ir.TableRead(
ir.TableNativeReader(resource('backward_compatability/1.0.0/table/0.ht')), False)
matrix_range = ir.MatrixRead(ir.MatrixRangeReader(1, 1, 10))
matrix_irs = [
ir.MatrixRepartition(matrix_range, 100, ir.RepartitionStrategy.SHUFFLE),
ir.MatrixUnionRows(matrix_range, matrix_range),
ir.MatrixDistinctByRow(matrix_range),
ir.MatrixRowsHead(matrix_read, 5),
ir.CastTableToMatrix(
ir.CastMatrixToTable(matrix_read, '__entries', '__cols'),
'__entries',
'__cols',
[]),
ir.MatrixAggregateRowsByKey(matrix_read, collect, collect),
ir.MatrixAggregateColsByKey(matrix_read, collect, collect),
matrix_read,
matrix_range,
ir.MatrixRead(ir.MatrixVCFReader(resource('sample.vcf'), ['GT'], hl.tfloat64, None, None, None, None,
False, True, False, True, None, None, None)),
ir.MatrixRead(ir.MatrixBGENReader(resource('example.8bits.bgen'), None, {}, 10, 1, 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'),
ir.MatrixAnnotateColsTable(matrix_read, table_read, '__foo'),
ir.MatrixToMatrixApply(matrix_read, {'name': 'MatrixFilterPartitions', 'parts': [0], 'keep': True})
]
for x in matrix_irs:
try:
Env.hail().expr.ir.IRParser.parse_matrix_ir(str(x))
except Exception as e:
raise ValueError(str(x)) from e
def matrix_irs(self):
hl.index_bgen(resource('example.8bits.bgen'),
reference_genome=hl.get_reference('GRCh37'),
contig_recoding={'01': '1'})
collect = ir.MakeStruct([('x', ir.ApplyAggOp('Collect', [], None, [ir.I32(0)]))])
matrix_read = ir.MatrixRead(
ir.MatrixNativeReader(
resource('backward_compatability/1.0.0/matrix_table/0.hmt'), None, False),
False, False)
table_read = ir.TableRead(
ir.TableNativeReader(resource('backward_compatability/1.0.0/table/0.ht'), None, False), False)
matrix_range = ir.MatrixRead(ir.MatrixRangeReader(1, 1, 10))
matrix_irs = [
ir.MatrixRepartition(matrix_range, 100, ir.RepartitionStrategy.SHUFFLE),
ir.MatrixUnionRows(matrix_range, matrix_range),
ir.MatrixDistinctByRow(matrix_range),
ir.MatrixRowsHead(matrix_read, 5),
ir.MatrixColsHead(matrix_read, 5),
ir.CastTableToMatrix(
ir.CastMatrixToTable(matrix_read, '__entries', '__cols'),
'__entries',
'__cols',
[]),
ir.MatrixAggregateRowsByKey(matrix_read, collect, collect),
ir.MatrixAggregateColsByKey(matrix_read, collect, collect),
matrix_read,
matrix_range,
ir.MatrixRead(ir.MatrixVCFReader(resource('sample.vcf'), ['GT'], hl.tfloat64, None, None, None, None,
False, True, False, True, None, None, None)),
ir.MatrixRead(ir.MatrixBGENReader(resource('example.8bits.bgen'), None, {}, 10, 1, 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.MatrixCollectColsByKey(matrix_read),
ir.MatrixExplodeRows(matrix_read, ['row_aset']),
ir.MatrixExplodeCols(matrix_read, ['col_aset']),
ir.MatrixAnnotateRowsTable(matrix_read, table_read, '__foo'),
ir.MatrixAnnotateColsTable(matrix_read, table_read, '__foo'),
ir.MatrixToMatrixApply(matrix_read, {'name': 'MatrixFilterPartitions', 'parts': [0], 'keep': True}),
ir.MatrixRename(matrix_read, {'global_f32': 'global_foo'}, {'col_f32': 'col_foo'}, {'row_aset': 'row_aset2'}, {'entry_f32': 'entry_foo'}),
ir.MatrixFilterIntervals(matrix_read, [hl.utils.Interval(hl.utils.Struct(row_idx=0), hl.utils.Struct(row_idx=10))], hl.tstruct(row_idx=hl.tint32), keep=False),
]
return matrix_irs
