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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
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I've added documentation in staging regarding this in PavlidisLab/Gemma@dcd7292.
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When no gene annotations are present on-disk, Gemma defaults to a simple format that lacks gene identifiers. This is breaking gemmapy.
The text was updated successfully, but these errors were encountered: