How to obtain the KEGG pathway a

script

import os
import json
import re

class KOParser(object):
    def __init__(self, map):
        self.map = map

    def json_parser(self):
        # check the existance of json file
        if os.path.exists(self.map):
            with open(self.map, 'r') as f:
                ko_list = []
                # convert json to dict
                map_dict = json.load(f)
                # print(type(map_dict)) dict
                maps = map_dict['children']
                # print(type(maps)) list
                for map in maps:
                    map_name = map['name'][0:5] + '\t' + map['name'][6:]
                    # print(map_name)
                    # print(type(map['children']))
                    for map_l_1 in map['children']:
                        map_l_1_name = map_l_1['name'][0:5] + '\t' + map_l_1['name'][6:]
                        # print(map_l_1_name)
                        for pathway in map_l_1['children']:
                            try:
                                for genes in pathway['children']:
                                    pathway_name = pathway['name'][0:5] + '\t' + pathway['name'][6:]
                                    # print(genes['name'])
                                    k_num = genes['name'].split(sep='  ')[0]
                                    gene_name = genes['name'].split(sep='  ')[1].split(sep=';')[0]
                                    anno = genes['name'].split(sep='  ')[1].split(sep=';')[-1]
                                    try:
                                        pattern = re.compile('(.*)(\[EC:.*\])')
                                        product = re.search(pattern, anno).group(1)
                                        ec = re.search(pattern, anno).group(2)
                                        ko = k_num + '\t' + gene_name + '\t' + product + '\t' + ec
                                    except:
                                        ko = k_num + '\t' + gene_name + '\t' + anno
                                    # print(ko)
                                    info = map_name + '\t' + map_l_1_name + '\t' + pathway_name + '\t' + ko
                                    ko_list.append(info)
                            except:
                                continue
                return ko_list
        else:
            print('Error: Json file does not exist.')

    def save_data(self, result, file_name):
        # convert list to string for writing as file
        for info in result:
            kos = ''.join(info) + '\n'
            with open(file_name, 'a', encoding='utf-8') as f:
                f.write(kos)


if __name__ == '__main__':
    map = 'ko00001.json'
    file_name = 'ko.txt'
    ko_json = KOParser(map)
    ko = ko_json.json_parser()
    ko_json.save_data(ko, file_name)

download json

choose Download json.

run

python pathway_annotation.py

Reference

1. 解析KEGG json文件