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#!/usr/bin/python
# coding: utf-8
# Author: LE YUAN
# Date: 2020-07-08 Run in python 3.7
import csv
with open("../../Data/database/Kcat_sabio.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 = set(data[3].split(';'))
EnzymeType = data[4]
PubMedID = data[5]
Organism =data[6]
UniprotID = data[7]
Value = data[8]
Unit = data[9]
Kcat_data_include_value.append([Type, ECNumber, Substrate, EnzymeType, PubMedID, Organism, UniprotID, Value, Unit])
Kcat_data.append([Type, ECNumber, Substrate, EnzymeType, PubMedID, Organism, UniprotID])
print(len(Kcat_data)) # 22416
new_lines = list()
for line in Kcat_data :
if line not in new_lines :
new_lines.append(line)
print(len(new_lines)) # 20344 included all elements, 16532 included all except for Kcat value and unit
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)
if unit in ['mol*s^(-1)*mol^(-1)', 's^(-', '-'] :
unit = 's^(-1)'
new_line[2] = ';'.join(list(new_line[2]))
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)) # 16484 after unifing the Kcat value unit to 's^(-1)', in which 15114 has a specific Unipro ID
with open("../../Data/database/Kcat_sabio_clean.tsv", "w") as outfile :
records = ['Type', 'ECNumber', 'Substrate', 'EnzymeType', 'PubMedID', 'Organism', 'UniprotID','Value', 'Unit']
outfile.write('\t'.join(records) + '\n')
for line in clean_Kcat :
outfile.write('\t'.join(line) + '\n')
# with open("../../Data/database/Kcat_sabio_clean.tsv", "wt") as outfile :
# tsv_writer = csv.writer(outfile, delimiter="\t")
# tsv_writer.writerow(["EntryID", "Type", "ECNumber", "Substrate", "EnzymeType", "PubMedID",
# "Organism", "UniprotID", "Value", "Unit"])
# import re
# string1 = 'MGTKGKVIKCKAAIAWEAGKPLCIEEVEVAPPKAHEVRIQIIATSLCHTDATVIDSKFEGLAFPVIVGHEAAGIVESIGPGVTNVKPGDKVIPLYAPLCRKCKFCLSPLTNLCGKISNLKSPASDQQLMEDKTSRFTCKGKPVYHFFGTSTFSQYTVVSDINLAKIDDDANLERVCLLGCGFSTGYGAAINNAKVTPGSTCAVFGLGGVGLSAVMGCKAAGASRIIGIDINSEKFVKAKALGATDCLNPRDLHKPIQEVIIELTKGGVDFALDCAGGSETMKAALDCTTAGWGSCTFIGVAAGSKGLTIFPEELIIGRTINGTFFGGWKSVDSIPKLVTDYKNKKFNLDALVTHTLPFDKISEAFDLMNQGKSVRTILIF'
# string2 = 'MGTKGKVIKCKAAIAWEAGKPLCIEEVEVAPPKAHEVRIQIIATSLCHTDATVIDSKFEG\
# LAFPVIVGHEAAGIVESIGPGVTNVKPGDKVIPLYAPLCRKCKFCLSPLTNLCGKISNLK\
# SPASDQQLMEDKTSRFTCKGKPVYHFFGTSTFSQYTVVSDINLAKIDDDANLERVCLLGC\
# GFSTGYGAAINNAKVTPGSTCAVFGLGGVGLSAVMGCKAAGASRIIGIDINSEKFVKAKA\
# LGATDCLNPRDLHKPIQEVIIELTKGGVDFALDCAGGSETMKAALDCTTAGWGSCTFIGV\
# AAGSKGLTIFPEELIIGRTINGTFFGGWKSVDSIPKLVTDYKNKKFNLDALVTHTLPFDK\
# ISEAFDLMNQGKSVRTILIF'
# print(string1.index('L'))
# n = [(i.start(), i.end()) for i in re.finditer('M', string2)]
# # [(0, 1), (129, 130), (215, 216), (281, 282), (368, 369)]
# print(n)
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