cameronmartino/bacdivepy

bacdivepy's Issues

outdated due to pandas

Looks like there is a bug due to renaming column names. This probably means that pandas will need to be either updated, or version fixed.

search_data=retrieve(['Ruminococcus', 'Oscillospira', 'Bacteroides', 'Lactobacillus',
                                 'Coprococcus', 'Clostridium', 'Parabacteroides', 'Alistipes', 
                                 'Roseburia', 'Prevotella'],
                                 search_type='genus')

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-12-b97e72b3c95c> in <module>
      2                                  'Coprococcus', 'Clostridium', 'Parabacteroides', 'Alistipes',
      3                                  'Roseburia', 'Prevotella'],
----> 4                                  search_type='genus')

~/miniconda3/envs/bacdivepy/lib/python3.7/site-packages/bacdive/DSMZClient.py in retrieve(search, search_type)
     59         build_final.append(flat_dfs)
     60 
---> 61     build_final = clean_cat(pd.DataFrame(build_final).T)
     62     return build_final
     63 

~/miniconda3/envs/bacdivepy/lib/python3.7/site-packages/bacdive/clean.py in clean_cat(search_data)
     16         subdf = search_data.loc[[x for x in search_data.index if id_ in x],:].dropna(axis=1)
     17         # fix col
---> 18         subdf.columns = ['DSM_'+id_]
     19         # fix index
     20         subdf.index = ['||'.join(x.split('||')[1:]) for x in subdf.index]

~/miniconda3/envs/bacdivepy/lib/python3.7/site-packages/pandas/core/generic.py in __setattr__(self, name, value)
   5078         try:
   5079             object.__getattribute__(self, name)
-> 5080             return object.__setattr__(self, name, value)
   5081         except AttributeError:
   5082             pass

pandas/_libs/properties.pyx in pandas._libs.properties.AxisProperty.__set__()

~/miniconda3/envs/bacdivepy/lib/python3.7/site-packages/pandas/core/generic.py in _set_axis(self, axis, labels)
    636 
    637     def _set_axis(self, axis, labels):
--> 638         self._data.set_axis(axis, labels)
    639         self._clear_item_cache()
    640 

~/miniconda3/envs/bacdivepy/lib/python3.7/site-packages/pandas/core/internals/managers.py in set_axis(self, axis, new_labels)
    153             raise ValueError(
    154                 'Length mismatch: Expected axis has {old} elements, new '
--> 155                 'values have {new} elements'.format(old=old_len, new=new_len))
    156 
    157         self.axes[axis] = new_labels

ValueError: Length mismatch: Expected axis has 0 elements, new values have 1 elements