While parsing the COSMIC database, we get:
/data/user/teo/devel/cancermuts/cancermuts/datasources.py:1678: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.
df_tmp = pd.read_csv(file, sep='\\t', dtype='str', na_values='NS', usecols=self._use_cols_database_files, encoding=self._encoding)
/data/user/teo/devel/cancermuts/cancermuts/datasources.py:1678: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.
df_tmp = pd.read_csv(file, sep='\\t', dtype='str', na_values='NS', usecols=self._use_cols_database_files, encoding=self._encoding)
in fact our call to read_csv uses sep='\\t', which the engine interprets as a regexp, which forces us into using the python parser which is significantly slower than the c parser. We should probably just have sep='\t' so we can take advantage of the c parser
While parsing the COSMIC database, we get:
in fact our call to
read_csvusessep='\\t', which the engine interprets as a regexp, which forces us into using thepythonparser which is significantly slower than thecparser. We should probably just havesep='\t'so we can take advantage of thecparser