sc.read_csv - 'ValueError: could not convert string to float'

[wdg118]

• [x] I have checked that this issue has not already been reported.
• [x] I have confirmed this bug exists on the latest version of scanpy.
• [ ] (optional) I have confirmed this bug exists on the master branch of scanpy.

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Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Minimal code sample (that we can copy&paste without having any data)

adata = sc.read_csv('/stanley/granger_lab_storage/Users/Will/120722_MOp_matrix_GABA_Glut_only_dropped_column.csv', delimiter = "\t")

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-43-462cb48f7ebe> in <module>
----> 1 adata = sc.read_csv('/stanley/granger_lab_storage/Users/Will/120722_MOp_matrix_GABA_Glut_only_dropped_column.csv', delimiter = "\t")

~/.local/lib/python3.8/site-packages/anndata/_io/read.py in read_csv(filename, delimiter, first_column_names, dtype)
     51         Numpy data type.
     52     """
---> 53     return read_text(filename, delimiter, first_column_names, dtype)
     54 
     55 

~/.local/lib/python3.8/site-packages/anndata/_io/read.py in read_text(filename, delimiter, first_column_names, dtype)
    358     else:
    359         with filename.open() as f:
--> 360             return _read_text(f, delimiter, first_column_names, dtype)
    361 
    362 

~/.local/lib/python3.8/site-packages/anndata/_io/read.py in _read_text(f, delimiter, first_column_names, dtype)
    423             data.append(np.array(line_list[1:], dtype=dtype))
    424         else:
--> 425             data.append(np.array(line_list, dtype=dtype))
    426         break
    427     # if row names are just integers

ValueError: could not convert string to float: 'AAACCTGAGGAGTCTG-L8TX_171026_01_F03'

Versions

anndata 0.8.0 scanpy 1.9.1

[Zethson]

Could you please paste a subset of the file? The header + 2 lines or so

[eroell]

We will close the issue for now, hopefully you obtained the expected behaviour :)

However, please don't hesitate to reopen this issue or create a new one if you have any more questions or run into any related problems in the future.

Thanks for being a part of our community! :)