Parse a file of strings in python separated by newline into a json array

Question

I have a file called path_text.txt its contents are the 2 strings separated by newline:

/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam 
/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam

I would like to have a json array object like this:

["/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam","/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam"]

I have tried something like this:

with open('path_text.txt','w',encoding='utf-8') as myfile:
    myfile.write(','.join('\n'))

But it does not work

You say you want to ***read*** the file to JSON, but your code is ***writing*** to the file. Which one are you actually trying to do? If you're trying to read, why not just `file.readlines()`? — Tomerikoo, Nov 12 '20 at 09:15
read yes. I'm sorry, I was trying to write comma (,) and double quotes (") into the existing file. thats why i used write — moth, Nov 12 '20 at 09:21
Does this answer your question? [How to read a file line-by-line into a list?](https://stackoverflow.com/questions/3277503/how-to-read-a-file-line-by-line-into-a-list) followed by [How do I write JSON data to a file?](https://stackoverflow.com/questions/12309269/how-do-i-write-json-data-to-a-file) — Tomerikoo, Nov 12 '20 at 09:28

Chase · Accepted Answer · 2020-11-12T10:11:39.647

I don't see where you're actually reading from the file in the first place. You have to actually read your path_text.txt before you can format it correctly right?

with open('path_text.txt','r',encoding='utf-8') as myfile:
    content = myfiel.read().splitlines()

Which will give you ['/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam', '/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam'] in content.

Now if you want to write this data to a file in the format ["/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam", "/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam"]-

import json

with open('path_json.json', 'w') as f:
    json.dump(content, f)

Now the path_json.json file looks like-

["/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam", "/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam"]

which is valid json in case you want to load a json from a file

@Tomerikoo true, I have no idea how I managed to forget using `json.dump` in my answer at first while simultaneously mentioning it in a comment — Chase, Nov 12 '20 at 10:12
@Chase yeah I noticed that in the moment ^_^ All good... now it looks fine :) — Tomerikoo, Nov 12 '20 at 10:13

score 3 · Answer 2 · answered Nov 12 '20 at 09:15

3

see below

with open('path_text.txt') as f:
    data = [l.strip() for l in f.readlines()]

answered Nov 12 '20 at 09:15

balderman

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1

list comprehension is good but note that single quotes are the result, JSON needs double quotes – moth Nov 12 '20 at 09:20
1

We have list of strings here. The quote type in not important. – balderman Nov 12 '20 at 09:22
2

@alex what? single quotes are just how python represent strings, that does not mean anything at all. That will still be valid json when you use `json.dumps` – Chase Nov 12 '20 at 09:22
1

@Chase I think the OP is confused with single-quotes ***when reading a file*** that can't be read as JSON – Tomerikoo Nov 12 '20 at 09:24
https://stackoverflow.com/questions/883243/does-json-parse-require-double-quoting – moth Nov 12 '20 at 09:25
JSON requires double quotes, guys I just want to copy and paste the result into a json file – moth Nov 12 '20 at 09:26
2

@alex then why don't you use the built-in `json` module? – Tomerikoo Nov 12 '20 at 09:26
@alex check my answer then – Chase Nov 12 '20 at 09:27
@Tomerikoo show me please how to do that with such file. would be great to see it. You mean `json.dump()` – moth Nov 12 '20 at 09:27

Parse a file of strings in python separated by newline into a json array

2 Answers2