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Save intermediate results #440
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Dear @wangjiawen2013 , the current simplest way to get over this that you can run Of course these are general advice, if you provide more details, we can address in more details. |
dyn.pp.recipe_monocle(adata) and dyn.cleanup(adata) cause the problem. I saves the adata after running dyn.pp.recipe_monocle(adata) and dyn.cleanup(adata), then load adata using dyn.read(adata), the following dyn.tl.dynamics cannot be performed. In [14]: dyn.tl.dynamics(adata,model="stochastic",cores=10)
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I found that after loading the adata, the 'tkey' and 'norm_method' (both the value is None) were lost ! In [22]: adata.write("test.h5ad") In [23]: adata = dyn.read("test.h5ad") In [24]: adata.uns['pp'] |
Perhaps it's a bug of anndata |
thanks! we will wait for the anndata team for a solution for now |
This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days |
Hi,
Dynamo performed well on my datasets. However, I have trouble on saving the results. Now there are intermediate results stored in adata.uns that can may lead to errors when writing the h5ad object. Sometimes I cannot run all dynamo pipeline at one time, so I must store the intermediate results and load it again another day to continue. In this case, I must store it in pickle file and load it another day. However, for some datasets the objects is too large for pickle to handle it (verflowError: cannot serialize a bytes object larger than 4 GiB). Hope we can save dynamo in h5ad without loss information.
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