Pandas update to 1.1 breaks load_PfamScan_results_dataframe

[tderond]

A user reached out describing an error they encountered:

<ipython-input-2-a0f501c7cad3> in load_PfamScan_results_dataframe(input_filename, verbose)
     11     if(verbose):
     12         print("loading "+input_filename)
---> 13     pfamscan_results_df=pandas.read_table(input_filename,
     14                                           delim_whitespace=True,
     15 #                                           dtype="str",

/ichec/work/nglif033c/miniconda3/envs/CO-ED/lib/python3.8/site-packages/pandas/io/parsers.py in read_table(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    753     float_precision=None,
    754 ):
--> 755     return read_csv(**locals())
    756 
    757 

/ichec/work/nglif033c/miniconda3/envs/CO-ED/lib/python3.8/site-packages/pandas/io/parsers.py in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    622 
    623     if delim_whitespace and delimiter != default_sep:
--> 624         raise ValueError(
    625             "Specified a delimiter with both sep and "
    626             "delim_whitespace=True; you can only specify one."

ValueError: Specified a delimiter with both sep and delim_whitespace=True; you can only specify one.

I could initially not replicate the error, but upon updating pandas from 1.0.3 to 1.1.1, I could.

[tderond]

This seems to be a bug in pandas: pandas-dev/pandas#35958

[tderond]

For now, replacing read_table in the load_PfamScan_results_dataframe function with read_csv (not changing anything else) seems to work as a workaround. Depending on how quickly this gets fixed on the Pandas side I may want to implement that fix here in the main branch.