Entering edit mode
5.6 years ago
Batu
▴
290
I have a loom file created from Seurat object by using as.loom function in Seurat3. After closing the file with $close.all(), I'm trying to read loom file by read_loom function in scanpy, but I have this error:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-7-aed61d3d5eef> in <module>
1 import scanpy as sc
----> 2 a = sc.read_loom('brain10x.loom')
/opt/conda/lib/python3.7/site-packages/anndata/readwrite/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names, dtype)
156
157 if X_name not in lc.layers.keys(): X_name = ''
--> 158 X = lc.layers[X_name].sparse().T.tocsr() if sparse else lc.layers[X_name][()].T
159
160 layers = OrderedDict()
/opt/conda/lib/python3.7/site-packages/loompy/loom_layer.py in sparse(self, rows, cols)
109 col: List[np.ndarray] = []
110 i = 0
--> 111 for (ix, selection, view) in self.ds.scan(items=cols, axis=1, layers=[self.name]):
112 if rows is not None:
113 vals = view.layers[self.name][rows, :]
/opt/conda/lib/python3.7/site-packages/loompy/loompy.py in scan(self, items, axis, layers, key, batch_size)
597 for key, layer in vals.items():
598 lm[key] = loompy.MemoryLoomLayer(key, layer)
--> 599 view = loompy.LoomView(lm, self.ra[ordering], self.ca[ix + selection], self.row_graphs[ordering], self.col_graphs[ix + selection], filename=self.filename, file_attrs=self.attrs)
600 yield (ix, ix + selection, view)
601 ix += cols_per_chunk
/opt/conda/lib/python3.7/site-packages/loompy/graph_manager.py in __getitem__(self, thing)
96 if type(thing) is slice or type(thing) is np.ndarray or type(thing) is int:
97 gm = GraphManager(None, axis=self.axis)
---> 98 for key, g in self.items():
99 # Slice the graph matrix properly without making it dense
100 (a, b, w) = (g.row, g.col, g.data)
/opt/conda/lib/python3.7/site-packages/loompy/graph_manager.py in items(self)
55 def items(self) -> Iterable[Tuple[str, sparse.coo_matrix]]:
56 for key in self.keys():
---> 57 yield (key, self[key])
58
59 def __len__(self) -> int:
/opt/conda/lib/python3.7/site-packages/loompy/graph_manager.py in __getitem__(self, thing)
116 raise AttributeError(f"'{type(self)}' object has no attribute {thing}")
117 else:
--> 118 return self.__getattr__(thing)
119
120 def __getattr__(self, name: str) -> sparse.coo_matrix:
/opt/conda/lib/python3.7/site-packages/loompy/graph_manager.py in __getattr__(self, name)
127 c = self.ds._file[a][name]["b"]
128 w = self.ds._file[a][name]["w"]
--> 129 g = sparse.coo_matrix((w, (r, c)), shape=(self.ds.shape[self.axis], self.ds.shape[self.axis]))
130 self.__dict__["storage"][name] = g
131 return g
/opt/conda/lib/python3.7/site-packages/scipy/sparse/coo.py in __init__(self, arg1, shape, dtype, copy)
190 self.data = self.data.astype(dtype, copy=False)
191
--> 192 self._check()
193
194 def reshape(self, *args, **kwargs):
/opt/conda/lib/python3.7/site-packages/scipy/sparse/coo.py in _check(self)
279 raise ValueError('row index exceeds matrix dimensions')
280 if self.col.max() >= self.shape[1]:
--> 281 raise ValueError('column index exceeds matrix dimensions')
282 if self.row.min() < 0:
283 raise ValueError('negative row index found')
ValueError: column index exceeds matrix dimensions
I can read loom file with loompy seamlessly. They are in the latest versions (Seurat_3.0.0.9000, loomR_0.2.1.9000, scanpy==1.4).
Should I add anything to the code below?:
a = scanpy.read_loom('brain10x.loom', sparse=True)
Thanks...
Yeah I've tried it before. I want to read loom to convert it into h5ad, when I open with
loompy.connect, it fails and gives this error: