Biopython provides a (bit unintuitive) API to access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). I am trying to make use of it, but the output is quite unhandy as a string. What is the best way to parse the data into a pandas.DataFrame()?

from Bio.KEGG import REST as Kegg
import io

  • $\begingroup$ It might be helpful if you provide an example of the output so it is easier understand why this string is not useful, and how it relates to your coded solution. $\endgroup$
    – user921
    Commented Apr 20, 2020 at 16:55

1 Answer 1


solution from @sören:

I came up with this solution for my problem:

from Bio.KEGG import REST as kegg

def _get_kegg(kegg_id):
    kegg_output = kegg.kegg_get(kegg_id).read()
    results = {}
    for line in kegg_output.split('\n'):
        splits = line.split()
        if not line.startswith(' '):    
            if len(splits) > 0:
                key = splits[0]
                value = ' '.join(splits[1:])
                results[key] = value
            results[key] += ' '.join(splits)
    return pd.DataFrame(results, index=[kegg_id])

_get_kegg_v = np.vectorize(_get_kegg)

def get_kegg_info(kegg_ids):
    if isinstance(kegg_ids, str):
        kegg_ids = [kegg_ids]
    return pd.concat(_get_kegg_v(kegg_ids), sort=False)

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