Create a JSON object in python

Question

I am trying to create a JSON object and appending it to a list but with no success. I got this error massage with:

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'

with the following code

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')

What did I miss?

Is that supposed to be part of the JSON document? Because it'll be dumped as an opaque string value. Not that it could ever be seen as valid JSON. — Martijn Pieters
– Martijn Pieters, Commented Oct 28, 2017 at 21:03

Elis Byberi · Accepted Answer · 2017-10-30 07:28:40Z

5

You are using json.dump() function wrong.

You pass an object and a file object:

json.dump(object, fileobject)

Use dict for key value mapping:

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')

edited Oct 30, 2017 at 7:28

answered Oct 28, 2017 at 21:40

Elis Byberi

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4 Comments

user977828 Over a year ago

Rather to get [{"source": {" would it be possible to get [["source": {" because I need it for this github.com/nicgirault/circosJS#chords?

Elis Byberi Over a year ago

You can not put a key-value pair inside a list/array. It would be an invalid JSON string. Please stop formatting JSON string by yourself.

user977828 Over a year ago

You right, how is it possible to write each list element in a new line?

Elis Byberi Over a year ago

Create another question with "How to pretty print JSON string in file?" Do not stress this question anymore.

Martijn Pieters · Accepted Answer · 2017-10-28 21:49:27Z

2

You need to double the { and } characters that are not placeholders; {id:...} is seen as a named placeholder otherwise:

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

The {{ and }} sequences end up as single { and } characters in the result.

Rather than put all your parts in separately, use numbered slots:

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

You should consider using the csv module to read your TSV data, and if you meant for the above data to be part of the JSON document (not as embedded string but as separate JSON arrays and objects), then formatting it as a string won't work.

You'll need to convert your CSV columns to integers first though:

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)

edited Oct 28, 2017 at 21:49

answered Oct 28, 2017 at 21:02

Martijn Pieters

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3 Comments

Elis Byberi Over a year ago

Why are you inserting object inside a list. What use would make using [{source:{}}]?

Martijn Pieters Over a year ago

@ElisByberi because that's what the string the OP was building contains. It's trivially dropped if not needed. Unfortunately the OP has not given and expected output or documentation on what they tried to produce.

Elis Byberi Over a year ago

Yes, I saw. This question is off-topic anyway.

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