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spio.cosmx appends path two times to the file name #298

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tsvvas opened this issue Apr 3, 2025 · 0 comments
Open

spio.cosmx appends path two times to the file name #298

tsvvas opened this issue Apr 3, 2025 · 0 comments

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@tsvvas
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tsvvas commented Apr 3, 2025

Hi spatialdata team,

It seems that the parser function for cosmx data appends path to the file name two times: first, when checking whether the file exists, and second, when reading the file:

counts_file = path / f"{dataset_id}_{CosmxKeys.COUNTS_SUFFIX}"
...
counts = pd.read_csv(path / counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)

This leads to the error when reading:

FileNotFoundError: [Errno 2] No such file or directory: '../cosmx_data/12345/../cosmx_data/12345/12345_exprMat_file.csv'

Best regards,
Vasily

mayank-singh-sikarwar added a commit to mayank-singh-sikarwar/spatialdata-io that referenced this issue Apr 29, 2025
mayank-singh-sikarwar added a commit to mayank-singh-sikarwar/spatialdata-io that referenced this issue Apr 29, 2025
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