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AMP-SCZ / outcome_calculations

Repository includes the scripts to calculate outcomes (predictors) for the AMP-SCZ study.
Apache License 2.0
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Error with newer Pandas #8

Open tashrifbillah opened 1 year ago

tashrifbillah commented 1 year ago

Just documenting, no action is necessary at this time since we have a working Python+Pandas:


$ python outcome_calculations.py "prescient" run_outcome
Traceback (most recent call last):
  File "/data/predict1/home/np487/amp_scz/outcome_calculations/outcome_calculations.py", line 473, in <module>
    ids = pd.read_csv('/data/pnl/home/gj936/U24/Clinical_qc/flowqc/REAL_DATA/{0}_sub_list.txt'.format(network), sep= '\n', index_col = False, header = None)
  File "/data/predict1/miniconda3/lib/python3.10/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/data/predict1/miniconda3/lib/python3.10/site-packages/pandas/util/_decorators.py", line 331, in wrapper
    return func(*args, **kwargs)
  File "/data/predict1/miniconda3/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 935, in read_csv
    kwds_defaults = _refine_defaults_read(
  File "/data/predict1/miniconda3/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 2063, in _refine_defaults_read
    raise ValueError(
ValueError: Specified \n as separator or delimiter. This forces the python engine which does not accept a line terminator. Hence it is not allowed to use the line terminator as separator.