diff --git a/setup.cfg b/setup.cfg index bda99a7..9c9c331 100644 --- a/setup.cfg +++ b/setup.cfg @@ -49,8 +49,8 @@ python_requires = >=3.8 # For more information, check out https://semver.org/. install_requires = importlib-metadata; python_version<"3.8" - dolomite-base>=0.2.4 - dolomite-se>=0.1.3 + dolomite-base>=0.3.0 + dolomite-se>=0.2.0 singlecellexperiment>=0.4.5 diff --git a/src/dolomite_sce/read_single_cell_experiment.py b/src/dolomite_sce/read_single_cell_experiment.py index 87cdda1..4e5857d 100644 --- a/src/dolomite_sce/read_single_cell_experiment.py +++ b/src/dolomite_sce/read_single_cell_experiment.py @@ -2,6 +2,7 @@ import os import dolomite_base as dl +import dolomite_se as dlse from dolomite_base.read_object import read_object_registry from singlecellexperiment import SingleCellExperiment @@ -36,8 +37,8 @@ def read_single_cell_experiment( with file-backed arrays in the assays. """ - metadata["type"] = "range_summarized_experiment" - rse = dl.alt_read_object(path, metadata=metadata, **kwargs) + # see comments in read_ranged_summarized_experiment in dolomite_se. + rse = dlse.read_ranged_summarized_experiment(path, metadata=metadata, **kwargs) _main_expt_name = None if "main_experiment_name" in metadata["single_cell_experiment"]: diff --git a/src/dolomite_sce/save_single_cell_experiment.py b/src/dolomite_sce/save_single_cell_experiment.py index 746d337..4e8981c 100644 --- a/src/dolomite_sce/save_single_cell_experiment.py +++ b/src/dolomite_sce/save_single_cell_experiment.py @@ -2,6 +2,7 @@ import os import dolomite_base as dl +import dolomite_se as dlse from singlecellexperiment import SingleCellExperiment from summarizedexperiment import RangedSummarizedExperiment @@ -63,18 +64,9 @@ def save_single_cell_experiment( if alt_expts_args is None: alt_expts_args = {} - ## Convert to RSE - _rse = RangedSummarizedExperiment( - assays=x.get_assays(), - row_data=x.get_row_data(), - column_data=x.get_column_data(), - row_ranges=x.get_row_ranges(), - row_names=x.get_row_names(), - column_names=x.get_column_names(), - metadata=x.get_metadata(), - ) - dl.alt_save_object( - _rse, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs + # see comments in save_ranged_summarized_experiment in dolomite_se. + dlse.save_ranged_summarized_experiment( + x, path, data_frame_args=data_frame_args, assay_args=assay_args, **kwargs ) # Modify OBJECT