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Don't use alt functions to read and save objects.
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This is simpler and avoids repeated calls to the override when traversing down
the SCE class hierarchy via save_object() and read_object().

This reverts commit 3960958.
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LTLA committed Oct 23, 2024
1 parent 3960958 commit 23f513d
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Showing 2 changed files with 7 additions and 14 deletions.
5 changes: 3 additions & 2 deletions src/dolomite_sce/read_single_cell_experiment.py
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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"]:
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16 changes: 4 additions & 12 deletions src/dolomite_sce/save_single_cell_experiment.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import os

import dolomite_base as dl
import dolomite_se as dlse
from singlecellexperiment import SingleCellExperiment
from summarizedexperiment import RangedSummarizedExperiment

Expand Down Expand Up @@ -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
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