I’m an amateur user of Python and the scverse ecosystem. I ran into an error with scirpy 0.18.0 that I don’t quite understand.
adata
AnnData object with n_obs × n_vars = 3618 × 16185
obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', ... 'sampleClusters', 'contigCellBarcode', 'barcode', 'CTgene', 'CTnt', 'CTaa', 'CTstrict', 'Frequency', 'cloneType', 'ident'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection'
uns: 'X_name', 'chain_indices', 'hvg', 'log1p'
obsm: 'airr', 'chain_indices'
layers: 'logcounts'
ir.tl.chain_qc(adata)
Error:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[37], line 1
----> 1 ir.tl.chain_qc(adata)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/tl/_chain_qc.py:86, in chain_qc(adata, airr_mod, airr_key, chain_idx_key, inplace, key_added)
83 res_receptor_type = np.empty(dtype=f"<U{string_length}", shape=(params.adata.shape[0],))
84 res_receptor_subtype = np.empty(dtype=f"<U{string_length}", shape=(params.adata.shape[0],))
---> 86 mask_has_ir = get._has_ir(params)
87 mask_multichain = mask_has_ir & ak.to_numpy(params.chain_indices["multichain"])
89 vj_loci = cast(np.ndarray, get.airr(params, "locus", ["VJ_1", "VJ_2"]).values)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/get/__init__.py:207, in _has_ir(params)
204 def _has_ir(params: DataHandler):
205 """Return a mask of all cells that have a valid IR configuration"""
206 return ak.to_numpy(
--> 207 (ak.count(params.chain_indices["VJ"], axis=1) + ak.count(params.chain_indices["VDJ"], axis=1)) > 0
208 )
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_operators.py:53, in _binary_method.<locals>.func(self, other)
51 if _disables_array_ufunc(other):
52 return NotImplemented
---> 53 return ufunc(self, other)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/highlevel.py:1511, in Array.__array_ufunc__(self, ufunc, method, *inputs, **kwargs)
1509 name = f"{type(ufunc).__module__}.{ufunc.__name__}.{method!s}"
1510 with ak._errors.OperationErrorContext(name, inputs, kwargs):
-> 1511 return ak._connect.numpy.array_ufunc(ufunc, method, inputs, kwargs)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_connect/numpy.py:466, in array_ufunc(ufunc, method, inputs, kwargs)
458 raise TypeError(
459 "no {}.{} overloads for custom types: {}".format(
460 type(ufunc).__module__, ufunc.__name__, ", ".join(error_message)
461 )
462 )
464 return None
--> 466 out = ak._broadcasting.broadcast_and_apply(
467 inputs, action, allow_records=False, function_name=ufunc.__name__
468 )
470 if len(out) == 1:
471 return wrap_layout(out[0], behavior=behavior, attrs=attrs)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_broadcasting.py:1140, in broadcast_and_apply(inputs, action, depth_context, lateral_context, allow_records, left_broadcast, right_broadcast, numpy_to_regular, regular_to_jagged, function_name, broadcast_parameters_rule)
1138 backend = backend_of(*inputs, coerce_to_common=False)
1139 isscalar = []
-> 1140 out = apply_step(
1141 backend,
1142 broadcast_pack(inputs, isscalar),
1143 action,
1144 0,
1145 depth_context,
1146 lateral_context,
1147 {
1148 "allow_records": allow_records,
1149 "left_broadcast": left_broadcast,
1150 "right_broadcast": right_broadcast,
1151 "numpy_to_regular": numpy_to_regular,
1152 "regular_to_jagged": regular_to_jagged,
1153 "function_name": function_name,
1154 "broadcast_parameters_rule": broadcast_parameters_rule,
1155 },
1156 )
1157 assert isinstance(out, tuple)
1158 return tuple(broadcast_unpack(x, isscalar) for x in out)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_broadcasting.py:1118, in apply_step(backend, inputs, action, depth, depth_context, lateral_context, options)
1116 return result
1117 elif result is None:
-> 1118 return continuation()
1119 else:
1120 raise AssertionError(result)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_broadcasting.py:1087, in apply_step.<locals>.continuation()
1085 # Any non-string list-types?
1086 elif any(x.is_list and not is_string_like(x) for x in contents):
-> 1087 return broadcast_any_list()
1089 # Any RecordArrays?
1090 elif any(x.is_record for x in contents):
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_broadcasting.py:623, in apply_step.<locals>.broadcast_any_list()
620 nextinputs.append(x)
621 nextparameters.append(NO_PARAMETERS)
--> 623 outcontent = apply_step(
624 backend,
625 nextinputs,
626 action,
627 depth + 1,
628 copy.copy(depth_context),
629 lateral_context,
630 options,
631 )
632 assert isinstance(outcontent, tuple)
633 parameters = parameters_factory(nextparameters, len(outcontent))
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_broadcasting.py:1100, in apply_step(backend, inputs, action, depth, depth_context, lateral_context, options)
1093 else:
1094 raise ValueError(
1095 "cannot broadcast: {}{}".format(
1096 ", ".join(repr(type(x)) for x in inputs), in_function(options)
1097 )
1098 )
-> 1100 result = action(
1101 inputs,
1102 depth=depth,
1103 depth_context=depth_context,
1104 lateral_context=lateral_context,
1105 continuation=continuation,
1106 backend=backend,
1107 options=options,
1108 )
1110 if isinstance(result, tuple) and all(isinstance(x, Content) for x in result):
1111 if any(content.backend is not backend for content in result):
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/awkward/_connect/numpy.py:458, in array_ufunc.<locals>.action(inputs, **ignore)
456 else:
457 error_message.append(type(x).__name__)
--> 458 raise TypeError(
459 "no {}.{} overloads for custom types: {}".format(
460 type(ufunc).__module__, ufunc.__name__, ", ".join(error_message)
461 )
462 )
464 return None
TypeError: no numpy.add overloads for custom types: AwkwardArrayView, AwkwardArrayView
This error occurred while calling
numpy.add.__call__(
<AwkwardArrayView [1, 2, 1, 1, 2, ..., 1, 2, 1, 1, 1] type='3618 * ...'>
<AwkwardArrayView [1, 1, 1, 1, 1, ..., 1, 1, 1, 2, 1] type='3618 * ...'>
)
Session info
Click to view session information
-----
anndata 0.10.8
awkward 2.6.9
matplotlib 3.9.2
natsort 8.4.0
numpy 2.0.2
pandas 2.2.3
scanpy 1.10.3
scipy 1.14.1
scirpy 0.18.0
seaborn 0.13.2
session_info 1.0.0
-----
Click to view modules imported as dependencies
Levenshtein 0.26.0
PIL 11.0.0
adjustText 1.2.0
airr 1.5.1
asttokens NA
awkward_cpp NA
backports NA
charset_normalizer 3.4.0
comm 0.2.2
cycler 0.12.1
cython_runtime NA
dateutil 2.9.0.post0
debugpy 1.8.7
decorator 5.1.1
executing 2.1.0
fsspec 2024.9.0
h5py 3.12.1
igraph 0.11.6
importlib_metadata NA
ipykernel 6.29.5
jaraco NA
jedi 0.19.1
joblib 1.4.2
kiwisolver 1.4.7
legacy_api_wrap NA
llvmlite 0.43.0
more_itertools 10.3.0
mpl_toolkits NA
mudata 0.3.1
networkx 3.4.1
numba 0.60.0
packaging 24.1
parso 0.8.4
patsy 0.5.6
pexpect 4.9.0
pkg_resources NA
platformdirs 4.3.6
pooch v1.8.2
prompt_toolkit 3.0.48
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pydev_ipython NA
pydevconsole NA
pydevd 3.1.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.18.0
pyparsing 3.2.0
pytz 2024.2
rapidfuzz 3.10.0
six 1.16.0
sklearn 1.5.2
stack_data 0.6.3
statsmodels 0.14.4
texttable 1.7.0
threadpoolctl 3.5.0
tornado 6.4.1
tqdm 4.66.5
tracerlib NA
traitlets 5.14.3
typing_extensions NA
wcwidth 0.2.13
yaml 6.0.2
yamlordereddictloader NA
zipp NA
zmq 26.2.0
zoneinfo NA
-----
IPython 8.28.0
jupyter_client 8.6.3
jupyter_core 5.7.2
-----
Python 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]
Linux-3.10.0-1160.118.1.el7.x86_64-x86_64-with-glibc2.17
-----
Session information updated at 2024-10-17 15:04