# Popv AssertionError: Don’t call \_normalize\_index with non-categorical/string names

**URL:** <https://discourse.scverse.org/t/popv-assertionerror-don-t-call-normalize-index-with-non-categorical-string-names/3672>\
**Category:** Help\
**Created:** [May 28, 2025, 9:48pm UTC](https://discourse.scverse.org/t/popv-assertionerror-don-t-call-normalize-index-with-non-categorical-string-names/3672 "2025-05-28T21:48:28Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![nembudziya](https://avatars.discourse-cdn.com/v4/letter/n/82dd89/32.png) [@nembudziya](https://discourse.scverse.org/u/nembudziya)\
**Post date:** [May 28, 2025, 9:48pm UTC](https://discourse.scverse.org/t/popv-assertionerror-don-t-call-normalize-index-with-non-categorical-string-names/3672/1 "2025-05-28T21:48:28Z")

</div>

Hello,

I am new to the scverse, and I am trying to annotate a query dataset with popv.

#### Dataset info

My query dataset is an AnnData object of publicly available 10X mouse pancreatic islets that I downloaded from the SRA. The datasets were merged after minimal processing (ambient RNA removal with `DecontX`, and doublet removal with `DoubletFinder`.

For the model, I am using `popV/tabula_muris_Pancreas_10x` from `HuggingFace`.

_\*To make the code cells more readable, I added the `>` symbol at the beginning of executed lines of code_

```python
# Step 2: Load your data (User Action Required)

> query_adata
AnnData object with n_obs × n_vars = 464747 × 27440
    obs: 'run', 'total_counts', 'n_genes_by_counts', 'sex', 'pct_counts_mt', 'cell_type', 'n_genes', 'doublet_score', 'predicted_doublet'
    uns: 'log1p'
    layers: 'counts'

# Preprocess the dataset
> query_adata.obs_names_make_unique()
> query_adata.var_names_make_unique()
> query_adata.X = query_adata.layers["counts"]
>
> query_adata.X.data
array([1., 1., 2., ..., 1., 18., 3.], dtype=float32)

```

#### Issue

I am getting stuck at step 4 of the example notebook where the execution stops with `AssertionError: Don’t call _normalize_index with non-categorical/string names`.

I put in safeguards to make sure my indices are the required data type, but it looks like the error pops up all the same. I am not sure if there’s something that I am missing in the dataset prep, or if this is just a bug.

```python
# Step 3 (User Action Required): Setting Up Annotation Parameters

> huggingface_repo = "popV/tabula_muris_Pancreas_10x"
> query_batch_key = "run"
> algorithms = None
> 
> query_adata.var['feature_name'] = query_adata.var_names.astype(str) # I added this line as the query_data has gene symbols

# Step 4: Perform annotation

> import numba
> 
> numba. __version__'0.61.0'

> hmo = popv.hub.HubModel.pull_from_huggingface_hub(huggingface_repo, cache_dir="tmp/tabula_muris")
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# The two lines below were added to try and mitigate the assertion error
> query_adata.obs.index = query_adata.obs.index.astype(str)
> query_adata.var.index = query_adata.var.index.astype(str)

> adata = hmo.annotate_data(query_adata, query_batch_key=query_batch_key, prediction_mode="inference", gene_symbols="feature_name")
INFO:cellxgene_census:The "stable" release is currently 2025-01-30. Specify 'census_version="2025-01-30"' in future calls to open_soma() to ensure data consistency.
SSSSSS
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
<ipython-input-41-41e85ddb159a> in <cell line: 0>()
----> 1 adata = hmo.annotate_data(
      2 query_adata,
      3 query_batch_key=query_batch_key,
      4 prediction_mode="inference", # "fast" does not integrate reference and query.
      5 gene_symbols="feature_name", # "Uncomment if using gene symbols."

5 frames
/usr/local/lib/python3.11/dist-packages/popv/hub/_model.py in annotate_data(self, query_adata, query_batch_key, save_path, prediction_mode, methods, gene_symbols)
    144 if gene_symbols is not None:
    145 print("SSSSSS")
--> 146 query_adata = self.map_genes(adata=query_adata, gene_symbols=gene_symbols)
    147 print("LLLLLL", self.local_dir, os.listdir(self.local_dir))
    148 

/usr/local/lib/python3.11/dist-packages/popv/hub/_model.py in map_genes(self, adata, gene_symbols)
    386 adata.var["old_index"] = adata.var_names
    387 adata.var_names = adata.var_names.map(feature_dict)
--> 388 adata = adata[:, adata.var.index.notna()].copy()
    389 return adata

/usr/local/lib/python3.11/dist-packages/anndata/_core/anndata.py in __getitem__ (self, index)
   1009 def __getitem__ (self, index: Index) -> AnnData:
   1010 """Returns a sliced view of the object."""
-> 1011 oidx, vidx = self._normalize_indices(index)
   1012 return AnnData(self, oidx=oidx, vidx=vidx, asview=True)
   1013 

/usr/local/lib/python3.11/dist-packages/anndata/_core/anndata.py in _normalize_indices(self, index)
    990 
    991 def _normalize_indices(self, index: Index | None) -> tuple[slice, slice]:
--> 992 return _normalize_indices(index, self.obs_names, self.var_names)
    993 
    994 # TODO: this is not quite complete...

/usr/local/lib/python3.11/dist-packages/anndata/_core/index.py in _normalize_indices(index, names0, names1)
     31 ax0, ax1 = unpack_index(index)
     32 ax0 = _normalize_index(ax0, names0)
---> 33 ax1 = _normalize_index(ax1, names1)
     34 return ax0, ax1
     35 

/usr/local/lib/python3.11/dist-packages/anndata/_core/index.py in _normalize_index(indexer, index)
     47 if not isinstance(index, pd.RangeIndex):
     48 msg = "Don’t call _normalize_index with non-categorical/string names"
---> 49 assert index.dtype != float, msg
     50 assert index.dtype != int, msg
     51 

AssertionError: Don’t call _normalize_index with non-categorical/string names

```

---

<div class="post-metadata">

**Author:** ![nembudziya](https://avatars.discourse-cdn.com/v4/letter/n/82dd89/32.png) [@nembudziya](https://discourse.scverse.org/u/nembudziya)\
**Post date:** [May 31, 2025, 12:28am UTC](https://discourse.scverse.org/t/popv-assertionerror-don-t-call-normalize-index-with-non-categorical-string-names/3672/2 "2025-05-31T00:28:05Z")

</div>

I was able to figure out the issue that was causing the error. In my case, my `query_data` object had gene symbols as `var_names`, so I changed those to Ensembl IDs and also made sure there were no duplicates. See [the Github issue I posted](https://github.com/YosefLab/popV/issues/91#issuecomment-2923776282) on the `popv` repository for more details.

The code works for now.