issue opening .loom file

[koalap-2018]

Hi guys,
I am trying to open a .loom file from : http://scope.aertslab.org/#/53d2bb24-9335-48d4-b874-eab05dd8c690/Aerts_Fly_AdultBrain_Filtered_57k.loom/gene

I can open the .loom file by:

loom_object = loompy.connect('Aerts_Fly_AdultBrain_Filtered_57k.loom', validate=False)

However i would like to open it with scanpy by:

loom_file = sc.read_loom('Aerts_Fly_AdultBrain_Filtered_57k.loom', validate=False)

and i get the following error:

---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-26-3a0e0ee3248f> in <module>()
----> 1 loom_file=sc.read_loom('Aerts_Fly_AdultBrain_Filtered_57k.loom',validate=False)

~\AppData\Local\Continuum\anaconda3\lib\site-packages\anndata\readwrite\read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names, dtype, **kwargs)
    184             var=var,
    185             layers=layers,
--> 186             dtype=dtype)
    187     return adata
    188 

~\AppData\Local\Continuum\anaconda3\lib\site-packages\anndata\base.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, oidx, vidx)
    670                 layers=layers,
    671                 dtype=dtype, shape=shape,
--> 672                 filename=filename, filemode=filemode)
    673 
    674     def _init_as_view(self, adata_ref: 'AnnData', oidx: Index, vidx: Index):

~\AppData\Local\Continuum\anaconda3\lib\site-packages\anndata\base.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, raw, layers, dtype, shape, filename, filemode)
    848         # annotations
    849         self._obs = _gen_dataframe(obs, self._n_obs,
--> 850                                    ['obs_names', 'row_names', 'smp_names'])
    851         self._var = _gen_dataframe(var, self._n_vars, ['var_names', 'col_names'])
    852 

~\AppData\Local\Continuum\anaconda3\lib\site-packages\anndata\base.py in _gen_dataframe(anno, length, index_names)
    285                 _anno = pd.DataFrame(
    286                     anno, index=anno[index_name],
--> 287                     columns=[k for k in anno.keys() if k != index_name])
    288                 break
    289         else:

~\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\frame.py in __init__(self, data, index, columns, dtype, copy)
    390                                  dtype=dtype, copy=copy)
    391         elif isinstance(data, dict):
--> 392             mgr = init_dict(data, index, columns, dtype=dtype)
    393         elif isinstance(data, ma.MaskedArray):
    394             import numpy.ma.mrecords as mrecords

~\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\internals\construction.py in init_dict(data, index, columns, dtype)
    210         arrays = [data[k] for k in keys]
    211 
--> 212     return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
    213 
    214 

~\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\internals\construction.py in arrays_to_mgr(arrays, arr_names, index, columns, dtype)
     54 
     55     # don't force copy because getting jammed in an ndarray anyway
---> 56     arrays = _homogenize(arrays, index, dtype)
     57 
     58     # from BlockManager perspective

~\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\internals\construction.py in _homogenize(data, index, dtype)
    275                 val = lib.fast_multiget(val, oindex.values, default=np.nan)
    276             val = sanitize_array(val, index, dtype=dtype, copy=False,
--> 277                                  raise_cast_failure=False)
    278 
    279         homogenized.append(val)

~\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\core\internals\construction.py in sanitize_array(data, index, dtype, copy, raise_cast_failure)
    656     elif subarr.ndim > 1:
    657         if isinstance(data, np.ndarray):
--> 658             raise Exception('Data must be 1-dimensional')
    659         else:
    660             subarr = com.asarray_tuplesafe(data, dtype=dtype)

Exception: Data must be 1-dimensional

[koalap-2018]

Hi guys,

I figure it out by creating a python 3.7.1 environment and updating the following libraries: numpy - 1.16.3 and scanpy - 1.4.1

[ivirshup]

Thanks for the update!