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Export to h5ad from BPCells based Seurat object

Open royfrancis opened this issue 1 year ago • 0 comments
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I get an error when trying to convert to h5ad from a BPCells based Seurat object.

> obj
An object of class Seurat 
30954 features across 17257 samples within 1 assay 
Active assay: RNA (30954 features, 0 variable features)
 1 layer present: counts

> SaveH5Seurat(obj, filename = "seurat-test.h5seurat")
Creating h5Seurat file for version 3.1.5.9900
Error in attr$write(robj) : HDF5-API Errors:
    error #000: ../../../src/H5A.c in H5Awrite(): line 629: null attribute buffer
        class: HDF5
        major: Invalid arguments to routine
        minor: Bad value

This is only an issue when working with BPCells based Seurat objects. Standard Seurat objects work fine.

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Seurat_5.0.0
SeuratObject_5.0.0
SeuratDisk_0.0.0.9021
BPCells_0.1.0

royfrancis avatar Nov 28 '23 12:11 royfrancis