Issue convert anndata to seurat object

[djlisko01]

hello all,

I've written the following code reference your youtube video:

However I get the following error when I try to load it into R using using Read10X from seurat:

Error in readMM(file = matrix.loc) :
'readMM()' is not yet implemented for representation 'array'

Any help is greatly appreciated!

Here's the code I wrote based on the youtube video (note I've tried different formats for the sparse matrix - int, int64, etc.)

• See attached file for reference

 @staticmethod
    def create_10x_files(adata, dir, raw_layer):
        RhapsodyReader.create_barcodes_table(adata=adata, save_path=f"{dir}/barcodes.tsv")
        RhapsodyReader.create_features_table(adata, f"{dir}/features.tsv")
        RhapsodyReader.create_matrix(adata, f"{dir}/matrix.mtx", layer=raw_layer)
        # RhapsodyReader.gzip_files_in_directory(dir)

    
    @staticmethod
    def create_matrix(adata, save_path, layer=None):
        if layer:
            matrix = adata.layers[layer].T
        else:
            matrix = adata.X.T
            
        io.mmwrite(save_path, matrix.astype(np.int64))

    @staticmethod
    def create_barcodes_table(adata, save_path):
        with open(save_path, "w") as file:
            for item in adata.obs_names:
                file.write(item + "\n")
    
    @staticmethod
    def create_features_table(adata, save_path):
        tab_var_names = ["\t".join([x, x, "Gene Expression"]) for x in adata.var_names]

        with open(save_path, "w") as file:
            for var_name in tab_var_names:
                file.write(var_name + "\n")

matrix.mtx.gz