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Comments (4)

cmoscardi avatar cmoscardi commented on August 26, 2024 1

Notes to self after fixing this. Or if anyone else wants to make a PR off this, feel free!

(is this library still maintained by anyone?)

  1. splitunc is deprecated. need to use splitdrive instead. source:
    https://github.com/aaronryank/-/blob/master/workspace/MSYS2_64/usr/lib/python3.4/ntpath.py

  2. Also need to change pd.DataFrame.from_items to pd.DataFrame.from_dict

from paratext.

Redevil10 avatar Redevil10 commented on August 26, 2024

I am having the same error:
AttributeError: module 'ntpath' has no attribute 'splitunc'

I am running this on Ubuntu

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arestifo avatar arestifo commented on August 26, 2024

I'm also getting the same error. I'm using MacOS 10.14.3

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/Applications/PyCharm.app/Contents/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/Applications/PyCharm.app/Contents/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/Users/restifo/PycharmProjects/bulk-rnaseq/util.py", line 5, in <module>
    df = paratext.load_csv_to_pandas("./data/TcgaTargetGtex_RSEM_Hugo_norm_count", num_threads=7)
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/paratext/core.py", line 403, in load_csv_to_pandas
    return pandas.DataFrame.from_items(expanded)
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/pandas/core/frame.py", line 1782, in from_items
    keys, values = lzip(*items)
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/paratext/core.py", line 355, in load_csv_to_expanded_columns
    for name, col, semantics, levels in load_raw_csv(filename, *args, **kwargs):
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/paratext/core.py", line 298, in load_raw_csv
    loader = internal_create_csv_loader(filename, *args, **kwargs)
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/paratext/core.py", line 188, in internal_create_csv_loader
    loader.load(_make_posix_filename(filename), params)
  File "/Users/restifo/anaconda3/envs/bulk-rnaseq/lib/python3.7/site-packages/paratext/core.py", line 120, in _make_posix_filename
    if ntpath.splitdrive(fn_or_uri)[0] or ntpath.splitunc(fn_or_uri)[0]:
AttributeError: module 'ntpath' has no attribute 'splitunc'

Python version:

> print(sys.version)
3.7.3 | packaged by conda-forge | (default, Mar 27 2019, 15:43:19) 
[Clang 4.0.1 (tags/RELEASE_401/final)]

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JamesFinlayson-zz avatar JamesFinlayson-zz commented on August 26, 2024

I'm having the same error with the same setup as @a-re . I'm also having the error when using load_csv_to_dict

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