fix #391: convert GEF gene names to Unicode in bins reader path#437
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fix #391: convert GEF gene names to Unicode in bins reader path#437cursor[bot] wants to merge 1 commit into
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The BgefR (bins) code path in read_gef() was not converting gene names
from byte strings to Unicode strings, unlike the CgefR (cell_bins) path
which already called .astype('U'). This caused all gene name comparisons
with Unicode-based reference data (e.g., H5AD files) to fail silently
in Python 3, since b'GeneX' != 'GeneX'.
Changes:
- stereo/io/reader.py: Add .astype('U') for gene_names and gene_id in
both the filtered and unfiltered BgefR code paths, matching the
existing CgefR behavior.
- stereo/algorithm/single_r/single_r.py: Improve the SingleR error
message to include sample gene names and their types from both test
and reference datasets for easier debugging.
Co-authored-by: wanruiwen-genomics-cn <wanruiwen-genomics-cn@users.noreply.github.com>
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Summary
When reading GEF files with
bin_type='bins', theBgefRreader path did not convert gene names from byte strings (returned bygefpy) to Unicode strings. This caused all downstream gene name comparisons — such as those in SingleR annotation — to fail silently, sinceb'GeneX' != 'GeneX'in Python 3. Thecell_binspath (CgefR) already performed this conversion correctly.Changes
stereo/io/reader.py: Added.astype('U')conversion forgene_namesandgene_idin both the filtered (gene_list/region) and unfiltered BgefR code paths, matching the existing CgefR behavior.stereo/algorithm/single_r/single_r.py: Improved the SingleR gene intersection error message to include sample gene names and their Python types from both test and reference datasets, making future debugging much easier.Verification
Classification
Closes #391