First you need to run clstr2txt (it comes with cd-hit). E.g.:

clstr2txt.pl BindingDBTargetSequences_100.fa.clstr > BindingDBTargetSequences_100_clusters.txt

Then, run the python code below, but change the variables (input and output file names):

import pandas as pd
from pandas import read_csv

clusters = read_csv('goa_swissprot_2020_100.fasta.clstr.txt', sep="\t")

single_clusters = clusters[clusters['clstr_size'] == 1]
multi_clusters = clusters[clusters['clstr_size'] != 1]

single_clusters['representitive_id'] = single_clusters['id']


def assign_cluster_representitive(cluster):
  representative = cluster[cluster['clstr_rep'] == 1]
  multi_clusters.loc[cluster.index,'representitive_id'] = representative['id'].values[0]

for cluster_name, cluster in multi_clusters.groupby('clstr'):
  assign_cluster_representitive(cluster)

clusters = pd.concat([single_clusters, multi_clusters])

clusters.to_csv('goa_swissprot_2020_100_with_representatives.clstr.txt', index=False)