Hi,
I keep getting an error " no fielded named ‘shape’." How should I continue?
thanks,
Morgan
# Load the BCR data
adata_bcr = ir.io.read_10x_vdj(
"/home/jovyan/shared/Morgan/unsortApr24_VDJ/outs/filtered_contig_annotations.csv" ,
filtered=True, include_fields=None
)
# Load the associated transcriptomics data
adata = sc.read_10x_h5("/home/jovyan/shared/Morgan/unsortApr24_GEX/scabranger/cellranger/multi/Ag/outs/per_sample_outs/Ag/count/sample_filtered_feature_bc_matrix.h5")
adata.var_names_make_unique()
_______________________________________________________________________________________
AttributeError Traceback (most recent call last)
Cell In[46], line 2
1 # Load the BCR data
----> 2 adata_bcr = ir.io.read_10x_vdj(
3 "/home/jovyan/shared/Morgan/unsortApr24_VDJ/outs/filtered_contig_annotations.csv" ,
4 filtered=True, include_fields=None
5 )
7 # Load the associated transcriptomics data
8 adata = sc.read_10x_h5("/home/jovyan/shared/Morgan/unsortApr24_GEX/scabranger/cellranger/multi/Ag/outs/per_sample_outs/Ag/count/sample_filtered_feature_bc_matrix.h5")
File /opt/conda/lib/python3.11/site-packages/scirpy/io/_io.py:240, in read_10x_vdj(path, filtered, include_fields, **kwargs)
237 else:
238 airr_cells = _read_10x_vdj_csv(path, filtered)
--> 240 return from_airr_cells(airr_cells, **kwargs)
File /opt/conda/lib/python3.11/site-packages/scirpy/io/_convert_anndata.py:50, in from_airr_cells(airr_cells, key_added)
44 obs.index = obs.index.astype(str)
46 obsm = {
47 key_added: ak.Array(c.chains for c in airr_cells),
48 }
---> 50 adata = AnnData(
51 X=None,
52 obs=obs,
53 obsm=obsm,
54 uns={"scirpy_version": version("scirpy")},
55 )
57 return adata
File /opt/conda/lib/python3.11/site-packages/anndata/_core/anndata.py:362, in AnnData.__init__(self, X, obs, var, uns, obsm, varm, layers, raw, dtype, shape, filename, filemode, asview, obsp, varp, oidx, vidx)
360 self._init_as_view(X, oidx, vidx)
361 else:
--> 362 self._init_as_actual(
363 X=X,
364 obs=obs,
365 var=var,
366 uns=uns,
367 obsm=obsm,
368 varm=varm,
369 raw=raw,
370 layers=layers,
371 dtype=dtype,
372 shape=shape,
373 obsp=obsp,
374 varp=varp,
375 filename=filename,
376 filemode=filemode,
377 )
File /opt/conda/lib/python3.11/site-packages/anndata/_core/anndata.py:564, in AnnData._init_as_actual(self, X, obs, var, uns, obsm, varm, varp, obsp, raw, layers, dtype, shape, filename, filemode)
561 self.uns = uns or OrderedDict()
563 # TODO: Think about consequences of making obsm a group in hdf
--> 564 self._obsm = AxisArrays(self, 0, vals=convert_to_dict(obsm))
565 self._varm = AxisArrays(self, 1, vals=convert_to_dict(varm))
567 self._obsp = PairwiseArrays(self, 0, vals=convert_to_dict(obsp))
File /opt/conda/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:288, in AxisArrays.__init__(self, parent, axis, vals)
286 self._data = dict()
287 if vals is not None:
--> 288 self.update(vals)
File <frozen _collections_abc>:949, in update(self, other, **kwds)
File /opt/conda/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:199, in AlignedActualMixin.__setitem__(self, key, value)
198 def __setitem__(self, key: str, value: V):
--> 199 value = self._validate_value(value, key)
200 self._data[key] = value
File /opt/conda/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:268, in AxisArraysBase._validate_value(self, val, key)
266 msg = "Index.equals and pd.testing.assert_index_equal disagree"
267 raise AssertionError(msg)
--> 268 return super()._validate_value(val, key)
File /opt/conda/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:72, in AlignedMapping._validate_value(self, val, key)
65 warn_once(
66 "Support for Awkward Arrays is currently experimental. "
67 "Behavior may change in the future. Please report any issues you may encounter!",
68 ExperimentalFeatureWarning,
69 # stacklevel=3,
70 )
71 for i, axis in enumerate(self.axes):
---> 72 if self.parent.shape[axis] == dim_len(val, i):
73 continue
74 right_shape = tuple(self.parent.shape[a] for a in self.axes)
File /opt/conda/lib/python3.11/functools.py:909, in singledispatch.<locals>.wrapper(*args, **kw)
905 if not args:
906 raise TypeError(f'{funcname} requires at least '
907 '1 positional argument')
--> 909 return dispatch(args[0].__class__)(*args, **kw)
File /opt/conda/lib/python3.11/site-packages/anndata/utils.py:109, in dim_len(x, axis)
102 @singledispatch
103 def dim_len(x, axis):
104 """\
105 Return the size of an array in dimension `axis`.
106
107 Returns None if `x` is an awkward array with variable length in the requested dimension.
108 """
--> 109 return x.shape[axis]
File /opt/conda/lib/python3.11/site-packages/awkward/highlevel.py:1239, in Array.__getattr__(self, where)
1234 raise AttributeError(
1235 f"while trying to get field {where!r}, an exception "
1236 f"occurred:\n{type(err)}: {err!s}"
1237 ) from err
1238 else:
-> 1239 raise AttributeError(f"no field named {where!r}")
AttributeError: no field named 'shape'