read_h5 bug

[Famingzhao]

Hi, I found a bug about converting adata to seurat using 'dior::write_h5' and 'dior::read_h5'

in Python: diopy.output.write_h5(adata, file ='data_annotation.h5', save_X=False)

in R:

basal.data <- dior::read_h5(file = "python.out.res/data_annotation.h5", assay.name = 'RNA', target.object = 'seurat')

<simpleError in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id, dataset_xfer_pl = dataset_xfer_pl, set_dim = TRUE, dim_to_set = dim_to_set, drop = drop): HDF5-API Errors: error #000: ../../../src/H5D.c in H5Dvlen_reclaim(): line 743: invalid argument class: HDF5 major: Invalid arguments to routine minor: Bad value

[fenghuijian]

Thank you very much for using our software! Sorry to reply to your message so late. Could you show me the structure of adata

[xing9133]

Thank you very much for using our software! Sorry to reply to your message so late. Could you show me the structure of adata

AnnData object with n_obs × n_vars = 34390 × 17642 obs: 'Sample', 'doublet', 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'condition', '_scvi_batch', '_scvi_labels', 'leiden', '_scvi_raw_norm_scaling', 'cell type', 'cell_type' var: 'n_cells' uns: 'Sample_colors', '_scvi_manager_uuid', '_scvi_uuid', 'cell type_colors', 'condition_colors', 'dendrogram_cell type', 'dendrogram_cell_type', 'dendrogram_leiden', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'scvi_markers', 'umap' obsm: 'X_pca', 'X_scVI', 'X_umap', '_scvi_extra_categorical_covs', '_scvi_extra_continuous_covs' layers: 'counts', 'scvi_normalized' obsp: 'connectivities', 'distances'

[MugenQin]

Thank you very much for using our software! Sorry to reply to your message so late. Could you show me the structure of adata

AnnData object with n_obs × n_vars = 34390 × 17642 obs: 'Sample', 'doublet', 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'condition', '_scvi_batch', '_scvi_labels', 'leiden', '_scvi_raw_norm_scaling', 'cell type', 'cell_type' var: 'n_cells' uns: 'Sample_colors', '_scvi_manager_uuid', '_scvi_uuid', 'cell type_colors', 'condition_colors', 'dendrogram_cell type', 'dendrogram_cell_type', 'dendrogram_leiden', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'scvi_markers', 'umap' obsm: 'X_pca', 'X_scVI', 'X_umap', '_scvi_extra_categorical_covs', '_scvi_extra_continuous_covs' layers: 'counts', 'scvi_normalized' obsp: 'connectivities', 'distances'

Hi, I had the same error. Did you solve your problem? How did you pass it?

[Lisa-Jammy]

Hi, I had the same error. Did you solve your problem? How do I solve it?

[Lisa-Jammy]

Thank you very much for using our software! Sorry to reply to your message so late. Could you show me the structure of adata

Can the author give some solution?

[fenghuijian]

Thank you very much for using our software, sorry for the late reply. Can you sample a small data and send it to this mail (fenghuijian@outlookcom)? And I check what the problem is. Thanks!

[Lisa-Jammy]

你好，我想问一下用dior这个包将scanpy的对象转为seurat对象转成功之后，无法进行基因的相关可视化并提示以上报错，这个问题应该如何解决呢？

	周莉莎 20192014031

@. | On 3/5/2023 @.> wrote：

Thank you very much for using our software, sorry for the late reply. Can you sample a small data and send it to this mail @.***)? And I check what the problem is. Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[fenghuijian]

您好！ 这个问题我也不太清楚，能否抽样一个数据（把一些信息去掉）让我检查一下。最近太多事情做了，实在抱歉！ 后期我们会对软件进行大幅度更细。欢迎继续使用！ 祝好！

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发件人: @.> 发送时间: 2023年3月6日 20:57 收件人: @.> 抄送: @.>; @.> 主题: Re: [JiekaiLab/scDIOR] read_h5 bug (Issue #7)

你好，我想问一下用dior这个包将scanpy的对象转为seurat对象转成功之后，无法进行基因的相关可视化并提示以上报错，这个问题应该如何解决呢？

	周莉莎 20192014031

@. | On 3/5/2023 @.> wrote：

Thank you very much for using our software, sorry for the late reply. Can you sample a small data and send it to this mail @.***)? And I check what the problem is. Thanks!

― Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

― Reply to this email directly, view it on GitHubhttps://github.com/JiekaiLab/scDIOR/issues/7#issuecomment-1456083109, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKNNSJER2QOIVXSTVMDVDATW2XNMJANCNFSM5XQKQSOA. You are receiving this because you commented.Message ID: @.***>