Hi!
I am trying to generate a particles.star file from an extract job in CS using csparc2star and I am getting this error:
/home/azken/local/pyem/pyem/metadata.py:334: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify ‘dtype=object’ when creating the ndarray
df[model[k]] = pd.DataFrame(np.array(
Columns must be same length as key
Traceback (most recent call last):
File “/home/azken/local/pyem/csparc2star.py”, line 42, in main
df = metadata.parse_cryosparc_2_cs(cs, passthroughs=args.input[1:], minphic=args.minphic,
File “/home/azken/local/pyem/pyem/metadata.py”, line 403, in parse_cryosparc_2_cs
df = cryosparc_2_cs_model_parameters(cs, df, minphic=minphic)
File “/home/azken/local/pyem/pyem/metadata.py”, line 334, in cryosparc_2_cs_model_parameters
df[model[k]] = pd.DataFrame(np.array(
File “/home/azken/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/core/frame.py”, line 3160, in setitem
self._setitem_array(key, value)
File “/home/azken/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/core/frame.py”, line 3189, in _setitem_array
raise ValueError(“Columns must be same length as key”)
ValueError: Columns must be same length as key
Required fields could not be mapped. Are you using the right input file(s)?
and this is the command I am using:
/local/pyem/csparc2star.py /cryosparc_project/P24/J198/extracted_particles.cs /cryosparc_project/P24/J198/P24_J198_passthrough_particles.cs particles_P24J198.star
Just a couple of months ago I did the same procedure successfully (same version of CS and pyem, and same command), so not sure what is going on here. Any help would be very much appreciated
Best,
Igor