Closed ViHammer closed 1 month ago
Running:
st.io.read_gef(file_path=gef_path, bin_size=bin_size, region=region)
and setting the region parameter to a region not covered by the <sample_name>.tissue.gef sample causes cryptic error:
<sample_name>.tissue.gef
[2024-06-01 11:46:22][Stereo][1662278][MainThread][140198435661632][reader][1070][INFO]: read_gef begin ... --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[17], line 1 ----> 1 st.io.read_gef(file_path=gef_path, 2 bin_size=bin_size, 3 region=region) File /.../mambaforge/envs/st/lib/python3.8/site-packages/stereo/utils/read_write_utils.py:37, in ReadWriteUtils.check_file_exists.<locals>.wrapped(*args, **kwargs) 35 else: 36 raise FileNotFoundError("Please ensure there is a file") ---> 37 return func(*args, **kwargs) File /.../mambaforge/envs/st/lib/python3.8/site-packages/stereo/io/reader.py:1191, in read_gef(file_path, bin_type, bin_size, is_sparse, gene_list, region, gene_name_index) 1187 cell_num = uniq_cell.size 1188 gene_num = gene_names.size 1190 data.position = np.array( -> 1191 list((zip(np.right_shift(uniq_cell, 32), np.bitwise_and(uniq_cell, 0xffffffff))))).astype('uint32') 1192 data.cells = Cell(cell_name=uniq_cell) 1194 exp_matrix = csr_matrix((count, (cell_ind, gene_ind)), shape=(cell_num, gene_num), dtype=np.uint32) TypeError: ufunc 'right_shift' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
With the correct region coordinates, no errors.
An easier to understand error message would help trouble shooting.
This error was caused by that no data can be extracted by the region you specified, we will improve the error message, thanks your feedback!
region
Running:
and setting the region parameter to a region not covered by the
<sample_name>.tissue.gef
sample causes cryptic error:With the correct region coordinates, no errors.
An easier to understand error message would help trouble shooting.