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failed for intron_group #8

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dipingxian431 opened this issue May 1, 2024 · 0 comments
Open

failed for intron_group #8

dipingxian431 opened this issue May 1, 2024 · 0 comments

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@dipingxian431
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Thank you for the tools.

When I run adata = group_introns(adata, by="three_prime"). there is an error report. Can you help me to solve it?

>>> adata = add_gene_annotation(adata, "/data/Mingchao/Reference/GRCh38_GTF_GENCODE/gencode.v44.basic.annotation.gtf")
Filtering to introns associated to 1 and only 1 gene.
/home/mingchao/miniconda3/envs/scQuint/lib/python3.12/site-packages/scquint/data.py:129: ImplicitModificationWarning: Trying to modify attribute `.var` of view, initializing view as actual.
  adata.var["gene_id"] = adata.var.gene_id_list
>>> adata = group_introns(adata, by="three_prime")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/mingchao/miniconda3/envs/scQuint/lib/python3.12/site-packages/scquint/data.py", line 141, in group_introns
    adata.var["intron_group"] = adata.var.apply(
    ~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/home/mingchao/miniconda3/envs/scQuint/lib/python3.12/site-packages/pandas/core/frame.py", line 4301, in __setitem__
    self._set_item_frame_value(key, value)
  File "/home/mingchao/miniconda3/envs/scQuint/lib/python3.12/site-packages/pandas/core/frame.py", line 4459, in _set_item_frame_value
    raise ValueError(
ValueError: Cannot set a DataFrame with multiple columns to the single column intron_group

Thank you so much.

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