/usr/local/bin/neoantigen/neoantigen.py:247: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. DONE
maf_df = pd.read_table(maf_file, comment='#', low_memory=False, header=0)
/usr/local/bin/neoantigen/neoantigen.py:339: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. DONE
netmhc_alleles = list(pd.read_table(netmhc4_alleleslist, header=None, usecols=[0])[0])
/usr/local/bin/neoantigen/neoantigen.py:391: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. DONE
np_df = pd.read_table(combined_output).drop_duplicates()
/usr/local/bin/neoantigen/neoantigen.py:459: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.
maf_output_df = pd.DataFrame.from_items([(s.name, s) for s in maf_output]).T
/usr/local/bin/neoantigen/neoantigen.py:462: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order.
predictions_output_df = pd.DataFrame.from_items([(s.name, s) for s in predictions_output]).T
The branch bugfix/pandas_warnings should address this
The branch
bugfix/pandas_warnings
should address this