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Error with loompy.loompy.combine

See original GitHub issue

I’m trying to combine loom files with the latest version of loompy (pulled from GitHub, commit d0bd1bd), but I get the following error. tissue_looms is a list of strings; combined_name is a string (enforced in the function call), so I don’t think I’m passing something wrong to combine.

loompy.loompy.combine(
        files=list(map(str, tissue_looms)), # type: List[str]
        output_file=str(combined_name) # type: str
)
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/loompy.py, line 377
<class 'bytes'>
Traceback (most recent call last):
  File "./merge_looms.py", line 111, in <module>
    main()
  File "./merge_looms.py", line 105, in main
    output_file=combined_name
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/loompy.py", line 933, in combine
    ds.add_loom(f, key, batch_size=batch_size)
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/loompy.py", line 381, in add_loom
    self.add_columns(vals, ca, fill_values=fill_values)
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/loompy.py", line 328, in add_columns
    self.ca[key] = np.concatenate([self.ca[key], vals])
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/attribute_manager.py", line 111, in __setitem__
    return self.__setattr__(name, val)
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/attribute_manager.py", line 129, in __setattr__
    values = loompy.normalize_attr_values(val)
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/normalize.py", line 72, in normalize_attr_values
    arr = normalize_attr_strings(arr)
  File "/usr/local/lib/python3.6/dist-packages/loompy-2.0.6-py3.6.egg/loompy/normalize.py", line 19, in normalize_attr_strings
    raise ValueError("Arbitrary numpy object arrays not supported (all elements must be string objects).")
ValueError: Arbitrary numpy object arrays not supported (all elements must be string objects).

Issue Analytics

State:
Created 6 years ago
Comments:8 (4 by maintainers)

Top GitHub Comments

1reaction

sejirocommented, Mar 2, 2018

I have just updated the package on our cluster and my initial checks indicate this newer version of loompy does indeed solve my problem. Thank you for the follow up! Really like the work between all of your labs, been working a lot with seurat and velocyto recently.

best, -Sejiro

0reactions

slinnarssoncommented, Mar 20, 2018

Great, good to know!

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