Hi, Im having a somewhat similar issue and wondered if you could help.
I have a scRNA seq dataset pre-processed in seurat, I have then used SeuratDisk to convert this into h5ad - named adata. I have also using scvelo made a loom file of this data - named ldata1. However I cannot seem to merge the two for further analysis. I cannot seem to work out the error message either? Any help/pointers really appreciated.
zincfingers89
commented
1 year ago
Hi, Im having a somewhat similar issue and wondered if you could help.
I have a scRNA seq dataset pre-processed in seurat, I have then used SeuratDisk to convert this into h5ad - named adata. I have also using scvelo made a loom file of this data - named ldata1. However I cannot seem to merge the two for further analysis. I cannot seem to work out the error message either? Any help/pointers really appreciated.
reload dataset
adata = sc.read_h5ad('data.h5ad')
adata
AnnData object with n_obs × n_vars = 11246 × 2000 obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'sample', 'group', 'sex', 'percent.mt', 'RNA_snn_res.0.5', 'seurat_clusters', 'barcode' var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable' uns: 'neighbors' obsm: 'X_pca', 'X_umap' varm: 'PCs' obsp: 'distances'
scv.settings.verbosity = 3 scv.settings.set_figure_params('scvelo', facecolor='white', dpi=100, frameon=False) cr.settings.verbosity = 2
ldata1 = scv.read('IM188-N.loom', cache=True) ldata1.var_names_make_unique()
ldata1
AnnData object with n_obs × n_vars = 2993 × 36601 obs: 'initial_size_unspliced', 'initial_size_spliced', 'initial_size' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand' layers: 'ambiguous', 'matrix', 'spliced', 'unspliced'
merge matrices into the original adata object
adata = scv.utils.merge(adata, ldata1)
UnboundLocalError Traceback (most recent call last) Cell In[10], line 2 1 # merge matrices into the original adata object ----> 2 adata = scv.utils.merge(adata, ldata1)
File /opt/anaconda3/lib/python3.8/site-packages/scvelo/core/_anndata.py:526, in merge(adata, ldata, copy, **kwargs) 524 if "id_length" in kwargs: 525 id_length = kwargs.get("id_length") --> 526 clean_obs_names(adata, id_length=id_length) 527 clean_obs_names(ldata, id_length=id_length) 528 common_obs = adata.obs_names.intersection(ldata.obs_names)
UnboundLocalError: local variable 'id_length' referenced before assignment