Passing a set as an indexer is not supported. Use a list instead.

[Meiyuhaha]

Hi Seppe,

I have an issue with this step:

consensus_peaks.to_bed(
    path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/consensus_regions.bed'),
    keep=True,
    compression='infer',
    chain=False)

TypeError                                 Traceback (most recent call last)
Cell In[26], line 1
----> 1 consensus_peaks.to_bed(
      2     path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/consensus_regions.bed'),
      3     keep=True,
      4     compression='infer',
      5     chain=False)

File /media/data1/zli/miniconda/envs/scenicplus/lib/python3.11/site-packages/pyranges/pyranges.py:4894, in PyRanges.to_bed(self, path, keep, compression, chain)
   4831 r"""Write to bed.
   4832 
   4833 Parameters
   (...)
   4890 ['chr1\t1\t5\t[.\t.\t](http://rna.ucsf.edu:8787/s/d6f2021f2ed724dc36a2a/lab/tree/scRNA/t./t)+\t1\n', 'chr1\t6\t8\t[.\t.\t-\t2\n](http://rna.ucsf.edu:8787/s/d6f2021f2ed724dc36a2a/lab/tree/scRNA/t./t-/t2/n)']
   4891 """
   4892 from pyranges.out import _to_bed
-> 4894 result = _to_bed(self, path, keep=keep, compression=compression)
   4896 if path and chain:
   4897     return self

File /media/data1/zli/miniconda/envs/scenicplus/lib/python3.11/site-packages/pyranges/out.py:129, in _to_bed(self, path, sep, keep, compression)
    126 gr = self
    128 outdfs = natsorted(gr.dfs.items())
--> 129 outdfs = [_bed(df, keep) for _, df in outdfs]
    131 if path:
    132     mode = "w+"

File /media/data1/zli/miniconda/envs/scenicplus/lib/python3.11/site-packages/pyranges/out.py:129, in <listcomp>(.0)
    126 gr = self
    128 outdfs = natsorted(gr.dfs.items())
--> 129 outdfs = [_bed(df, keep) for _, df in outdfs]
    131 if path:
    132     mode = "w+"

File /media/data1/zli/miniconda/envs/scenicplus/lib/python3.11/site-packages/pyranges/out.py:37, in _bed(df, keep)
     34 noncanonical = set(df.columns) - set(all_columns)
     36 if keep:
---> 37     return pd.concat([outdf, df.get(noncanonical)], axis=1)
     38 else:
     39     return outdf

File ~/.local/lib/python3.11/site-packages/pandas/core/generic.py:4581, in NDFrame.get(self, key, default)
   4528 """
   4529 Get item from object for given key (ex: DataFrame column).
   4530 
   (...)
   4578 '[unknown]'
   4579 """
   4580 try:
-> 4581     return self[key]
   4582 except (KeyError, ValueError, IndexError):
   4583     return default

File ~/.local/lib/python3.11/site-packages/pandas/core/frame.py:4063, in DataFrame.__getitem__(self, key)
   4062 def __getitem__(self, key):
-> 4063     check_dict_or_set_indexers(key)
   4064     key = lib.item_from_zerodim(key)
   4065     key = com.apply_if_callable(key, self)

File ~/.local/lib/python3.11/site-packages/pandas/core/indexing.py:2774, in check_dict_or_set_indexers(key)
   2766 """
   2767 Check if the indexer is or contains a dict or set, which is no longer allowed.
   2768 """
   2769 if (
   2770     isinstance(key, set)
   2771     or isinstance(key, tuple)
   2772     and any(isinstance(x, set) for x in key)
   2773 ):
-> 2774     raise TypeError(
   2775         "Passing a set as an indexer is not supported. Use a list instead."
   2776     )
   2778 if (
   2779     isinstance(key, dict)
   2780     or isinstance(key, tuple)
   2781     and any(isinstance(x, dict) for x in key)
   2782 ):
   2783     raise TypeError(
   2784         "Passing a dict as an indexer is not supported. Use a list instead."
   2785     )

TypeError: Passing a set as an indexer is not supported. Use a list instead.

Much appreciated!

[SeppeDeWinter]

Hi @Meiyuhaha

This seems to be an incompatibility between pandas and pyranges.

What versions do you have for both packages?

Best,

Seppe

[Meiyuhaha]

Hi @SeppeDeWinter ,

Thank you for your reply.

The versions of the packages are:

pandas 1.5.0 pyranges 0.0.111

Now I also have another trouble when I run the scenicplus pipline:

TypeError: descriptor 'call' for 'type' objects doesn't apply to a 'property' object [Fri May 17 23:59:25 2024] Error in rule region_to_gene: jobid: 10 input: /home/zli/outputs/ACC_GEX.h5mu, /home/zli/outputs/search_space.tsv output: /home/zli/outputs/region_to_gene_adj.tsv shell:

    scenicplus grn_inference region_to_gene             --multiome_mudata_fname /home/zli/outputs/ACC_GEX.h5mu             --search_space_fname /home/zli/outputs/search_space.tsv             --temp_dir /home/zli/outputs/tmp             --out_region_to_gene_adjacencies /home/zli/outputs/region_to_gene_adj.tsv             --importance_scoring_method GBM             --correlation_scoring_method SR             --n_cpu 40

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-05-17T235847.987448.snakemake.log WorkflowError: At least one job did not complete successfully.

Looking forward to your reply. Thank you!

[SeppeDeWinter]

Hi @Meiyuhaha

Is this the full error log? Could you please post the full log, I'm not able to see where things go wrong here.

Best,

Seppe

[HeleneZhao]

Hi, I have the same issue. this is the command: consensus_peaks.to_bed( path = os.path.join(out_dir, "consensus_peak_calling/consensus_regions.bed"), keep =True, compression = 'infer', chain = False)

this the error:

TypeError: Passing a set as an indexer is not supported. Use a list instead.

pandas 1.5.0 pyranges 0.0.111

and I think the problem is what you said, there is an incompatibility between pandas and pyranges. other packages also the same problem, like https://github.com/pm4py/pm4py-core/issues/486 any chance the support team could help with this problem

thanks

Best Helene