在 python 中创建一个 JSON 对象

Question

我正在尝试创建一个 JSON 对象并将其附加到列表中，但没有成功。我得到了这个错误信息：

Traceback (most recent call last):
  File "/projects/circos/test.py", line 32, in <module>
    read_relationship('data/chr03_small_n10.blast')
  File "/projects/circos/test.py", line 20, in read_relationship
    tmp = ("[source: {id: '{}',start: {},end: {}},target: {id: '{}',start: {}, end: {}}],").format(parts[0],parts[2],parts[3],parts[1],parts[4],parts[5])
KeyError: 'id'

使用以下代码

def read_relationship(filename):
    data = []
    with open(filename) as f:
        f.next()
        for line in f:
            try:
                parts = line.rstrip().split('\t')
                query_name = parts[0]
                subject_name = parts[1]
                query_start = parts[2]
                query_end = parts[3]
                subject_start = parts[4]
                subject_end = parts[5]


                # I need: [source: {id: 'Locus_1', start: 1, end: 1054}, target: {id: 'tig00007234', start: 140511, end: 137383}],
                tmp = ("[source: {id: '{}',start: {},end: {}},target: {id: '{}',start: {}, end: {}}],").format(parts[0],parts[2],parts[3],parts[1],parts[4],parts[5])
                data.append(tmp)

            except ValueError:
                pass

    with open('data/data.txt', 'w') as outfile:
        json.dump(data, outfile)


read_relationship('data/chr03_small_n10.blast')

我错过了什么？

Answer 1

您需要双倍 { 和 } 非占位符的字符； {id:...} 被视为命名占位符，否则：

tmp = (
    "[source: {{id: '{}',start: {},end: {}}},"
    "target: {{id: '{}',start: {}, end: {}}}],").format(
        parts[0], parts[2], parts[3], parts[1], parts[4], parts[5])

{{ 和 }} 序列在结果中以单个 { 和 } 字符结束。

与其将所有零件分开放置，不如使用带编号的插槽：

tmp = (
    "[source: {{id: '{0}',start: {2},end: {3}}},"
    "target: {{id: '{1}',start: {4}, end: {5}}}],").format(
        *parts)

您应该考虑使用 csv 模块来读取您的 TSV 数据，如果您打算将上述数据作为 JSON 文档的一部分（不是作为嵌入字符串而是作为单独的 JSON 数组和对象），然后将其格式化为字符串将不起作用。

不过，您需要先将 CSV 列转换为整数：

import csv
import json

def read_relationship(filename):
    data = []
    with open(filename, 'rb') as f:
        reader = csv.reader(f, delimiter='\t')
        next(reader, None)
        for row in reader:
            data.append([{
                'source': {
                    'id': row[0],
                    'start': int(row[2]),
                    'end': int(row[3]),
                },
                'target': {
                    'id': row[1],
                    'start': int(row[4]),
                    'end': int(row[5]),
                },
            }])

    with open('data/data.txt', 'w') as outfile:
        json.dump(data, outfile)

Answer 2

您使用的 json.dump() 函数有误。

您传递了一个对象和一个文件对象：

json.dump(object, fileobject)

使用字典进行键值映射：

def read_relationship(filename):
    data = []
    with open(filename) as f:
        f.next()
        for line in f:
            try:
                parts = line.rstrip().split('\t')
                query_name = parts[0]
                subject_name = parts[1]
                query_start = parts[2]
                query_end = parts[3]
                subject_start = parts[4]
                subject_end = parts[5]

                # use dict here
                item = {
                    'source': {
                        'id': query_name,
                        'start': subject_name,
                        'end': query_start
                },
                    'target': {
                        'id': query_end,
                        'start': subject_start,
                        'end': subject_end
                    }
                }
                data.append(item)

            except ValueError:
                pass

    with open('data/data.txt', 'w') as outfile:
        json.dump(data, outfile)


read_relationship('data/chr03_small_n10.blast')

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