ov.single.cytotrace2 bug

[qbly27]

AttributeError: 'float' object has no attribute 'upper'

I have already found the error.

The code does not work. duplicate_genes = [i for i in duplicate_genes if i is not np.nan]

so the duplicate_genes has many nan. When NaN appears as a column name, its data type is a floating point number type.

Looking forward to you fixing this bug.

details are above

---

AttributeError Traceback (most recent call last)
Cell In[13], line 1
----> 1 results = ov.single.cytotrace2(adata,
2 use_model_dir="./cytotrace2/5_models_weights",
3 species="human",
4 batch_size = 10000,
5 smooth_batch_size = 1000,
6 disable_parallelization = False,
7 max_cores = None,
8 max_pcs = 200,
9 seed = 14,
10 output_dir = './'
11 )

File ~/miniconda3/envs/ov/lib/python3.11/site-packages/omicverse/single/_cytotrace2.py:207, in cytotrace2(adata, use_model_dir, species, batch_size, smooth_batch_size, disable_parallelization, max_cores, max_pcs, seed, output_dir)
201 results.append(executor.submit(process_subset, idx,
202 chunked_expression, smooth_batch_size,
203 smooth_cores_to_use, species,
204 use_model_dir, output_dir, max_pcs, seed))
206 for f in concurrent.futures.as_completed(results):
--> 207 smooth_by_knn_df = f.result()
208 predictions.append(smooth_by_knn_df)
212 for idx in range(chunk_number):

File ~/miniconda3/envs/ov/lib/python3.11/concurrent/futures/_base.py:449, in Future.result(self, timeout)
447 raise CancelledError()
448 elif self._state == FINISHED:
--> 449 return self.__get_result()
451 self._condition.wait(timeout)
453 if self._state in [CANCELLED, CANCELLED_AND_NOTIFIED]:

File ~/miniconda3/envs/ov/lib/python3.11/concurrent/futures/_base.py:401, in Future.__get_result(self)
399 if self._exception:
400 try:
--> 401 raise self._exception
402 finally:
403 # Break a reference cycle with the exception in self._exception
404 self = None

File ~/miniconda3/envs/ov/lib/python3.11/concurrent/futures/thread.py:58, in _WorkItem.run(self)
55 return
57 try:
---> 58 result = self.fn(*self.args, **self.kwargs)
59 except BaseException as exc:
60 self.future.set_exception(exc)

File ~/miniconda3/envs/ov/lib/python3.11/site-packages/omicverse/single/_cytotrace2.py:21, in process_subset(idx, chunked_expression, smooth_batch_size, smooth_cores_to_use, species, use_model_dir, output_dir, max_pcs, seed)
17 def process_subset(idx, chunked_expression, smooth_batch_size, smooth_cores_to_use,
18 species, use_model_dir, output_dir, max_pcs, seed):
19
20 # map and rank
---> 21 cell_names, gene_names, ranked_data = preprocess(chunked_expression, species)
23 # top variable genes
24 top_col_inds = top_var_genes(ranked_data)

File ~/miniconda3/envs/ov/lib/python3.11/site-packages/omicverse/externel/cytotrace2/gen_utils.py:121, in preprocess(expression, species)
119 duplicate_genes = expression.columns[expression.columns.duplicated()].values
120 duplicate_genes = [i for i in duplicate_genes if i is not np.nan]
--> 121 idx = [unmapped_genes[i.upper()] for i in duplicate_genes if i.upper() in unmapped_genes.keys()]
122 expression = expression.iloc[:, [j for j, c in enumerate(expression.columns) if j not in idx]]
124 else:

File ~/miniconda3/envs/ov/lib/python3.11/site-packages/omicverse/externel/cytotrace2/gen_utils.py:121, in (.0)
119 duplicate_genes = expression.columns[expression.columns.duplicated()].values
120 duplicate_genes = [i for i in duplicate_genes if i is not np.nan]
--> 121 idx = [unmapped_genes[i.upper()] for i in duplicate_genes if i.upper() in unmapped_genes.keys()]
122 expression = expression.iloc[:, [j for j, c in enumerate(expression.columns) if j not in idx]]
124 else:

AttributeError: 'float' object has no attribute 'upper'

[Starlitnightly]

#116