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taylor-lab / neoantigen-dev

neoantigen prediction from WES/WGS
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Feature/bug fix: remove pandas warnings #5

Closed evanbiederstedt closed 5 years ago

evanbiederstedt commented 5 years ago 
/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

evanbiederstedt commented 5 years ago

Addressed here: https://github.com/taylor-lab/neoantigen-dev/pull/6