anndata

lilab-bcb · Sep 17, 2024 · d620c40 · d620c40
1 parent ddbc98a
commit d620c40
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Showing 3 changed files with 12 additions and 386 deletions.
diff --git a/cirrocumulus/abstract_backed_dataset.py b/cirrocumulus/abstract_backed_dataset.py
@@ -3,10 +3,10 @@
 import pandas as pd
 import scipy.sparse
 from anndata import AnnData
+from anndata._core.sparse_dataset import sparse_dataset
 
 from cirrocumulus.abstract_dataset import AbstractDataset
 from cirrocumulus.anndata_util import ADATA_LAYERS_UNS_KEY, ADATA_MODULE_UNS_KEY
-from cirrocumulus.sparse_dataset import SparseDataset
 
 
 # string_dtype = h5py.check_string_dtype(dataset.dtype)
@@ -73,8 +73,8 @@ def get_X(self, var_ids, keys, node):
             get_item = var_ids.get_indexer_for(keys)
 
         if self.is_group(node):
-            sparse_dataset = SparseDataset(node)  # sparse
-            X = sparse_dataset[:, get_item]
+            ds = sparse_dataset(node)  # sparse
+            X = ds[:, get_item]
         else:  # dense
             X = self.slice_dense_array(node, get_item)
         var = pd.DataFrame(index=keys)

diff --git a/cirrocumulus/sparse_dataset.py b/cirrocumulus/sparse_dataset.py