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#!/usr/bin/python
# coding: utf-8
# Author: LE YUAN
# Date: 2020-06-25
# This script is to extract Kcat data from all EC files into one file.
import os
import csv
import re
outfile = open("../../Data/database/Kcat_brenda.tsv", "wt")
# with open("./Kcat_sabio.tsv", "wt") as outfile :
tsv_writer = csv.writer(outfile, delimiter="\t")
tsv_writer.writerow(["EntryID", "Type", "ECNumber", "Substrate", 'EnzymeType', "Organism","Value", "Unit"])
filenames = os.listdir('../../Data/database/Kcat_brenda')
# print(len(filenames)) # 3339 EC files
i = 0
j = 0
for filename in filenames :
print(filename[2:-4])
if filename != '.DS_Store' :
with open("../../Data/database/Kcat_brenda/%s" %(filename), 'r', encoding="utf-8") as file :
lines = file.readlines()
for line in lines[1:] :
data = line.strip().split('\t')
value = float(data[2])
desc = data[4]
# print(desc)
if value > 0 : # Kcat value should not be less than 0, but there exist some weird values, less than 0.
# print(value)
# print(type(value))
i += 1
if 'mutant' in desc or 'mutated' in desc:
# print(desc)
mutant = re.findall('[A-Z]\d+[A-Z]', desc) # re is of great use
# print(mutant)
if len(mutant) >=1 :
enzymeType = '/'.join(mutant)
else :
continue
# print(desc)
# j += 1
# print(j)
# enzymeType = 'wildtype'
# print('------------------------------------------------')
else :
enzymeType = 'wildtype'
tsv_writer.writerow([i, 'kcat', filename[2:-4], data[3], enzymeType, data[1], str(value), 's^(-1)'])
outfile.close()
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