Stream 1.1 Error #136
Description
Hello,
I'm having trouble upgrading the version of STREAM. While before I had no errors, now none of my scripts work.
I work with conda environments and here is the version of the main packages:
With STREAM 1.0 (where everything is fine) :
print(stream.__version__)
print(scanpy.__version__)
print(pandas.__version__)
print(matplotlib.__version__)
print(numpy.__version__)
1.0
1.6.0
1.0.5
3.2.2
1.19.2
But when I upgrade only the stream package to 1.1 I have the following error :
stream.filter_features(adata,min_n_cells = 5, assay = 'rna')
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/tmp/ipykernel_977625/1328372756.py in <module>
----> 1 st.filter_features(adata,min_n_cells = 5, assay = 'rna')
~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/stream/core.py in filter_features(adata, min_n_cells, max_n_cells, min_pct_cells, max_pct_cells, min_n_counts, max_n_counts, expr_cutoff, assay)
627 else:
628 n_counts = np.sum(adata.X,axis=0).astype(int)
--> 629 adata.var['n_counts'] = n_counts
630 if('n_cells' in adata.var_keys()):
631 n_cells = adata.var['n_cells']
~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in __setitem__(self, key, value)
2936 else:
2937 # set column
-> 2938 self._set_item(key, value)
2939
2940 def _setitem_slice(self, key, value):
~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value)
2998
2999 self._ensure_valid_index(value)
-> 3000 value = self._sanitize_column(key, value)
3001 NDFrame._set_item(self, key, value)
3002
~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, key, value, broadcast)
3634
3635 # turn me into an ndarray
-> 3636 value = sanitize_index(value, self.index, copy=False)
3637 if not isinstance(value, (np.ndarray, Index)):
3638 if isinstance(value, list) and len(value) > 0:
~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/internals/construction.py in sanitize_index(data, index, copy)
609
610 if len(data) != len(index):
--> 611 raise ValueError("Length of values does not match length of index")
612
613 if isinstance(data, ABCIndexClass) and not copy:
ValueError: Length of values does not match length of index
I also tried to create another conda environment by only fixing the version of STREAM :
print(stream.__version__)
print(scanpy.__version__)
print(pandas.__version__)
print(matplotlib.__version__)
print(numpy.__version__)
1.1
1.6.0
1.3.5
3.5.0
1.20.3
But I have about the same error when I run stream.filter_features(adata,min_n_cells = 5, assay = 'rna') :
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/tmp/ipykernel_978038/1328372756.py in <module>
----> 1 st.filter_features(adata,min_n_cells = 5, assay = 'rna')
~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/stream/core.py in filter_features(adata, min_n_cells, max_n_cells, min_pct_cells, max_pct_cells, min_n_counts, max_n_counts, expr_cutoff, assay)
627 else:
628 n_counts = np.sum(adata.X,axis=0).astype(int)
--> 629 adata.var['n_counts'] = n_counts
630 if('n_cells' in adata.var_keys()):
631 n_cells = adata.var['n_cells']
~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in __setitem__(self, key, value)
3610 else:
3611 # set column
-> 3612 self._set_item(key, value)
3613
3614 def _setitem_slice(self, key: slice, value):
~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value)
3782 ensure homogeneity.
3783 """
-> 3784 value = self._sanitize_column(value)
3785
3786 if (
~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, value)
4507
4508 if is_list_like(value):
-> 4509 com.require_length_match(value, self.index)
4510 return sanitize_array(value, self.index, copy=True, allow_2d=True)
4511
~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/common.py in require_length_match(data, index)
530 if len(data) != len(index):
531 raise ValueError(
--> 532 "Length of values "
533 f"({len(data)}) "
534 "does not match length of index "
ValueError: Length of values (1) does not match length of index (32738)
And it's seems to be a numpy error but I am not very familiar with python...
What do you recommend for a functional STREAM 1.1 environment?
Best,
Lea