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#!/usr/bin/python
# coding: utf-8
# Author: LE YUAN
# Date: 2020-07-09 Run in python 3.7
# This script is to clean Kcat data extracted from BRENDA database
import csv
with open("../../Data/database/Kcat_brenda.tsv", "r", encoding='utf-8') as file :
lines = file.readlines()[1:]
Kcat_data = list()
Kcat_data_include_value = list()
for line in lines :
# print(line)
data = line.strip().split('\t')
Type = data[1]
ECNumber = data[2]
Substrate = data[3]
EnzymeType = data[4]
Organism =data[5]
Value = data[6]
Unit = data[7]
Kcat_data_include_value.append([Type, ECNumber, Substrate, EnzymeType, Organism, Value, Unit])
Kcat_data.append([Type, ECNumber, Substrate, EnzymeType, Organism])
print(len(Kcat_data)) # 69140, in which 22723 mutant 46417 wildtype
new_lines = list()
for line in Kcat_data :
if line not in new_lines :
new_lines.append(line)
print(len(new_lines)) # 67566 included all elements, 52390 included all except for Kcat value and unit, 32305 if further not include enzymeType
i = 0
clean_Kcat = list()
for new_line in new_lines :
# print(new_line)
i += 1
print(i)
value_unit = dict()
Kcat_values = list()
for line in Kcat_data_include_value :
if line[:-2] == new_line :
value = line[-2]
value_unit[str(float(value))] = line[-1]
# print(type(value)) # <class 'str'>
Kcat_values.append(float(value))
# print(value_unit)
# print(Kcat_values)
max_value = max(Kcat_values) # choose the maximum one for duplication Kcat value under the same entry as the data what we use
unit = value_unit[str(max_value)]
# print(max_value)
# print(unit)
new_line.append(str(max_value))
new_line.append(unit)
if new_line[-1] == 's^(-1)' :
clean_Kcat.append(new_line)
# print(clean_Kcat)
print(len(clean_Kcat)) # 52390
with open("../../Data/database/Kcat_brenda_clean.tsv", "w") as outfile :
records = ['Type', 'ECNumber', 'Substrate', 'EnzymeType', 'Organism', 'Value', 'Unit']
outfile.write('\t'.join(records) + '\n')
for line in clean_Kcat :
outfile.write('\t'.join(line) + '\n')
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