When no gene annotations are present on-disk, Gemma defaults to a simple format that lacks gene identifiers. This is breaking gemmapy.
.tox/py/lib/python3.12/site-packages/gemmapy/gemmapy_api.py:1460: in get_dataset_object
expression = {k:get_exp(k) for k in unique_sets}
.tox/py/lib/python3.12/site-packages/gemmapy/gemmapy_api.py:1418: in get_exp
exp = exp[~exp.GeneSymbol.str.contains("|",regex = False,na = True)]
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Probe GBM: 40L GBM: 96E GBM: 46A15 GBM: 99A6 GBM: 64A5 GBM: 32A6 GBM: 4A10 GBM: 5A4 GBM: 52A28 ... ... 0.514 0.487 0.725 0.624 0.181 0.411 0.201 0.081
[33600 rows x 39 columns]
name = 'GeneSymbol'
@final
def __getattr__(self, name: str):
"""
After regular attribute access, try looking up the name
This allows simpler access to columns for interactive use.
"""
# Note: obj.x will always call obj.__getattribute__('x') prior to
# calling obj.__getattr__('x').
if (
name not in self._internal_names_set
and name not in self._metadata
and name not in self._accessors
and self._info_axis._can_hold_identifiers_and_holds_name(name)
):
return self[name]
> return object.__getattribute__(self, name)
E AttributeError: 'DataFrame' object has no attribute 'GeneSymbol'
.tox/py/lib64/python3.12/site-packages/pandas/core/generic.py:6299: AttributeError
When no gene annotations are present on-disk, Gemma defaults to a simple format that lacks gene identifiers. This is breaking gemmapy.