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