read_loom failed

[mbuttner]

Hi,
I use scanpy 1.3.1. I have tried the 'read_loom' function, but it produced the following error:

adata = sc.read(filename=path_to_velocyto_files + 'all_controls.loom')

--> This might be very slow. Consider passing `cache=True`, which enables much faster reading from a cache file.
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-52-61a36c9ba297> in <module>()
----> 1 adata = sc.read(filename=path_to_velocyto_files + 'all_controls.loom')

~/anaconda3/lib/python3.6/site-packages/scanpy/readwrite.py in read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, **kwargs)
     73         return _read(filename, backed=backed, sheet=sheet, ext=ext,
     74                      delimiter=delimiter, first_column_names=first_column_names,
---> 75                      backup_url=backup_url, cache=cache, **kwargs)
     76     # generate filename and read to dict
     77     filekey = filename

~/anaconda3/lib/python3.6/site-packages/scanpy/readwrite.py in _read(filename, backed, sheet, ext, delimiter, first_column_names, backup_url, cache, suppress_cache_warning, **kwargs)
    311             adata = _read_softgz(filename)
    312         elif ext == 'loom':
--> 313             adata = read_loom(filename=filename, **kwargs)
    314         else:
    315             raise ValueError('Unkown extension {}.'.format(ext))

~/anaconda3/lib/python3.6/site-packages/anndata/readwrite/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names)
    144     filename = fspath(filename)  # allow passing pathlib.Path objects
    145     from loompy import connect
--> 146     with connect(filename, 'r') as lc:
    147 
    148         if X_name not in lc.layers.keys(): X_name = ''

AttributeError: __enter__

I have found that when I try to read the file the interactive console, I have the following result:

> filename =os.fspath(path_to_velocyto_files + 'all_controls.loom')
> lc =connect(filename, 'r')
> lc.layer.keys()
dict_keys(['', 'ambiguous', 'spliced', 'unspliced'])

So for my loom file, it's not 'layers', but 'layer'. Can you consider to include this case in the anndata read function?

[flying-sheep]

connect returns a LoomConnection object. Support for the with syntax (=the __enter__/__exit__ methods) was added to LoomConnection in linnarsson-lab/loompy@aaafe0c. On top of the commit page, you see which tags (versions) contain this commit:

Looks like you have an ancient loompy version <1.1.0, is that correct?

[mbuttner]

Erm, apparently working with loompy 1.0.0. I guess that I may solve my issues by updating?

[falexwolf]

Yes!

[flying-sheep]

Great!

[mbuttner]

Ok, updated to loompy 2.0.12:

adata = sc.read_loom(filename=path_to_velocyto_files + 'all_controls.loom')

Variable names are not unique. To make them unique, call `.var_names_make_unique`.
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-8-de63a2957df4> in <module>()
----> 1 adata = sc.read_loom(filename=path_to_velocyto_files + 'all_controls.loom')

~/anaconda3/lib/python3.6/site-packages/anndata/readwrite/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names)
    172             obs=obs,  # not ideal: make the generator a dict...
    173             var=var,
--> 174             layers=layers)
    175     return adata
    176 

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, oidx, vidx)
    681                 layers=layers,
    682                 dtype=dtype, shape=shape,
--> 683                 filename=filename, filemode=filemode)
    684 
    685     def _init_as_view(self, adata_ref: 'AnnData', oidx: Index, vidx: Index):

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, raw, layers, dtype, shape, filename, filemode)
    901         self._clean_up_old_format(uns)
    902 
--> 903         self._layers = AnnDataLayers(self, layers, dtype)
    904 
    905     def __sizeof__(self):

~/anaconda3/lib/python3.6/site-packages/anndata/layers.py in __init__(self, adata, layers, dtype, adata_ref, oidx, vidx)
     31                     raise ValueError('Shape does not fit.')
     32                 if layers[key].dtype != np.dtype(dtype):
---> 33                     self._layers[key] = layers[key].astype(dtype, copy=False)
     34                 else:
     35                     self._layers[key] = layers[key]

TypeError: astype() got an unexpected keyword argument 'copy'

[flying-sheep]

Can you try the newest anndata from git?

pip install -U git+https://github.com/theislab/anndata.git

It should give you a better error message

[mbuttner]

OK, so I updated anndata to '0.6.10+2.ga323978' and re-run the read_loom command.

adata = sc.read_loom(filename=path_to_velocyto_files + 'all_controls.loom')

Variable names are not unique. To make them unique, call `.var_names_make_unique`.
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-de63a2957df4> in <module>()
----> 1 adata = sc.read_loom(filename=path_to_velocyto_files + 'all_controls.loom')

~/anaconda3/lib/python3.6/site-packages/anndata/readwrite/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names)
    172             obs=obs,  # not ideal: make the generator a dict...
    173             var=var,
--> 174             layers=layers)
    175     return adata
    176 

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in __init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, oidx, vidx)
    681                 layers=layers,
    682                 dtype=dtype, shape=shape,
--> 683                 filename=filename, filemode=filemode)
    684 
    685     def _init_as_view(self, adata_ref: 'AnnData', oidx: Index, vidx: Index):

~/anaconda3/lib/python3.6/site-packages/anndata/base.py in _init_as_actual(self, X, obs, var, uns, obsm, varm, raw, layers, dtype, shape, filename, filemode)
    901         self._clean_up_old_format(uns)
    902 
--> 903         self._layers = AnnDataLayers(self, layers, dtype)
    904 
    905     def __sizeof__(self):

~/anaconda3/lib/python3.6/site-packages/anndata/layers.py in __init__(self, adata, layers, dtype, adata_ref, oidx, vidx)
     35                 raise ValueError('Shape does not fit.')
     36             if layer.dtype != np.dtype(dtype):
---> 37                 self._layers[key] = layer.astype(dtype, copy=False)
     38             else:
     39                 self._layers[key] = layer

TypeError: astype() got an unexpected keyword argument 'copy'

[flying-sheep]

OK. I test if layer is a np.ndarray (which has .astype with copy) or a scipy.sparse.spmatrix (which also has .astype with copy)

for the sparse matrices, this was added in scipy/scipy@d09dc32, which ended up in scipy 1.0, released almost a year ago. do you also have an old scipy version?

[mbuttner]

OK, my scipy version is 0.19.1.

[yojetsharma]

Hi, I am facing a similar issue too.
When I processed my spliced and unspliced using Velocyto and loaded those loom files, it worked. But when
I converted my seurat to loom and I tried loading it into velocyto but received the following error:

>>> ls003 = scv.read_loom('/home/praghu/yojetsharma/new/loom_files/ls003/ls003.loom')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/anndata/compat/__init__.py", line 305, in inner_f
    return f(*args, **kwargs)
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/anndata/_io/read.py", line 251, in read_loom
    with connect(filename, "r", **kwargs) as lc:
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/loompy/loompy.py", line 1515, in connect
    return LoomConnection(filename, mode, validate=validate)
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/loompy/loompy.py", line 85, in __init__
    if not lv.validate(filename):
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/loompy/loom_validator.py", line 50, in validate
    self.version = get_loom_spec_version(f)
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/loompy/utils.py", line 19, in get_loom_spec_version
    if "attrs" in f and "LOOM_SPEC_VERSION" in f["/attrs"]:
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/praghu/yojetsharma/.conda/envs/yojet_velo/lib/python3.10/site-packages/h5py/_hl/group.py", line 483, in __contains__
    return self._e(name) in self.id
  File "h5py/h5g.pyx", line 466, in h5py.h5g.GroupID.__contains__
  File "h5py/h5g.pyx", line 467, in h5py.h5g.GroupID.__contains__
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5g.pyx", line 540, in h5py.h5g._path_valid
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5l.pyx", line 212, in h5py.h5l.LinkProxy.exists
RuntimeError: Unable to get link info (addr overflow, addr = 12416, size = 176, eoa = 2048)