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theosanderson / taxonium

A tool for exploring very large trees in the browser
http://taxonium.org
GNU General Public License v3.0
95 stars 17 forks source link

Parsing NS file #572

Closed Biophylo2001 closed 5 months ago

Biophylo2001 commented 5 months ago

so i used UShER commands to make a .pb MAT file. I converted that to Json file using this command : usher_to_taxonium --input global_assignments.pb --output gb.json

Then I uploaded the resulted json file to Taxonium browser, but it's the screen is showing 'Parsing NS file' and has been buffering for more than an hour now and i still see no tree made. What's wrong?

theosanderson commented 5 months ago

Hi @Sanyukta2001,

usher_to_taxonium actually outputs technically not json but jsonl or ndjson (https://jsonlines.org/).

I recommend using the .jsonl extension. 

usher_to_taxonium --input global_assignments.pb --output gb.jsonl

If you use that, Taxonium will automatically detect that you are uploading a Taxonium format file.

If you upload with the .json extension then by default Taxonium assumes this is a JSON file as outputted by Nextstrain tools, which means it will parse the file incorrectly.

Alternatively, if you didn't want to rename your file you would need to choose "Taxonium JSONL" in the dropdown:

image

Hope this helps, let us know if you still have problems.