| #!/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) | |