bug loading vizgen data
Open
@michalk8 is already working on this.
Since Mar 24, 2023.
I/O :cd:
sdata compat :milky_way:
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- Python
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Description
Description
Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9
Minimal reproducible example
adata = sq.read.vizgen(
path=data_path,
counts_file=os.path.join(data_path,section,file_path,cbg_file),
meta_file=os.path.join(data_path,section,file_path,meta_file),
transformation_file=os.path.join(data_path,section,'region_0/images/micron_to_mosaic_pixel_transform.csv'),
)
Traceback
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [54], in <cell line: 1>()
----> 1 adata = sq.read.vizgen(
2 path=data_path,
3 counts_file=os.path.join(data_path,section,file_path,cbg_file),
4 meta_file=os.path.join(data_path,section,file_path,meta_file),
5 transformation_file=os.path.join(data_path,section,'region_0/images/micron_to_mosaic_pixel_transform.csv'),
6 )
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/squidpy/read/_read.py:146, in vizgen(path, counts_file, meta_file, transformation_file, library_id, **kwargs)
144 # fmt: off
145 coords = pd.read_csv(path / meta_file, header=0, index_col=0)
--> 146 coords.columns = ["fov", "volume", "center_x", "center_y", "min_x", "max_x", "min_y", "max_y"]
147 # fmt: on
149 adata.obs = pd.merge(adata.obs, coords, how="left", left_index=True, right_index=True)
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/pandas/core/generic.py:5588, in NDFrame.__setattr__(self, name, value)
5586 try:
5587 object.__getattribute__(self, name)
-> 5588 return object.__setattr__(self, name, value)
5589 except AttributeError:
5590 pass
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/pandas/_libs/properties.pyx:70, in pandas._libs.properties.AxisProperty.__set__()
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/pandas/core/generic.py:769, in NDFrame._set_axis(self, axis, labels)
767 def _set_axis(self, axis: int, labels: Index) -> None:
768 labels = ensure_index(labels)
--> 769 self._mgr.set_axis(axis, labels)
770 self._clear_item_cache()
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/pandas/core/internals/managers.py:214, in BaseBlockManager.set_axis(self, axis, new_labels)
212 def set_axis(self, axis: int, new_labels: Index) -> None:
213 # Caller is responsible for ensuring we have an Index object.
--> 214 self._validate_set_axis(axis, new_labels)
215 self.axes[axis] = new_labels
File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/miniconda3/envs/scvi-tool/lib/python3.9/site-packages/pandas/core/internals/base.py:69, in DataManager._validate_set_axis(self, axis, new_labels)
66 pass
68 elif new_len != old_len:
---> 69 raise ValueError(
70 f"Length mismatch: Expected axis has {old_len} elements, new "
71 f"values have {new_len} elements"
72 )
ValueError: Length mismatch: Expected axis has 9 elements, new values have 8 elements
Version
'1.2.2'
...
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