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Fix coercion issue from RSE to SE #107

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Merged
jkanche merged 2 commits into from
Sep 1, 2026
Merged

Fix coercion issue from RSE to SE #107

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21fc295
don't use pandas for coercion
jkanche Sep 1, 2026
592f5f9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 1, 2026
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22 changes: 17 additions & 5 deletions src/summarizedexperiment/RangedSummarizedExperiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -980,17 +980,29 @@ def to_summarizedexperiment(self):
import copy

if isinstance(self._row_ranges, CompressedGenomicRangesList):
df = self._row_ranges.get_unlist_data().to_pandas()
gr = self._row_ranges.get_unlist_data()
else:
df = self._row_ranges.to_pandas()
gr = self._row_ranges

range_bf = biocframe.BiocFrame.from_pandas(df)
if new_row_data is None or new_row_data.shape[0] == 0:
range_dict = {
"seqnames": gr.get_seqnames(),
"starts": gr.get_start(),
"ends": gr.get_end(),
"strand": gr.get_strand(as_type="list"),
}

if gr.mcols is not None:
for col in gr.mcols.column_names:
range_dict[col] = gr.mcols.column(col)

range_bf = biocframe.BiocFrame(range_dict, number_of_rows=len(gr), row_names=gr.get_names())

if new_row_data is None or new_row_data.shape[0] == 0 or len(new_row_data.column_names) == 0:
new_row_data = range_bf
else:
new_row_data = copy.copy(new_row_data)
for col in range_bf.column_names:
new_row_data[col] = range_bf[col]
new_row_data.set_column(col, range_bf.column(col), in_place=True)
except Exception as e:
warn(f"Failed to transfer row_ranges to row_data: {e}", UserWarning)

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