Python script to just take the top ChEMBL hit for each query gene, and any hits with E-values within 1e+5 of it. Also, only take hits of E-value <= 1e-10:

format_blastp_output_for_chembl_besthitonly.py

import os
import sys
from collections import defaultdict
import FiftyHG_Chembl

#====================================================================#

def main():

    # find the blast output files:  
    blastoutput = defaultdict()
    mydir = os.getcwd() # the current directory
    myfiles = os.listdir(mydir)
    for myfile in myfiles:
        if myfile.endswith('.txt') and 'chembl' not in myfile: # eg. schistosoma_mansoni.txt. 
            # find the species name:
            temp = myfile.split('.txt')
            species = temp[0] # eg. schistosoma_mansoni

            # parse and format this blast output file, to just take the top blast match of a helminth gene, considering
            # all the splice-forms of a helminth gene:
            myfile = os.path.join(mydir, myfile)
            output_file = '%s2' % myfile 
            print('Making file',output_file)
            if not os.path.exists(output_file):  
                FiftyHG_Chembl.reformat_blast_output_besthitonly(myfile,species,output_file,1e-10)                 
 
    print("FINISHED\n")

#====================================================================#

if __name__=="__main__":
    main()

#====================================================================#