Generate files for taxonium
Project description
Taxonium tools
Taxonium tools is a Python utility that allows you to generate Taxonium format files from UShER mutation-annoated trees.
Installation
pip install taxoniumtools
Usage
Basic run
First get some files:
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.meta.tsv.gz
wget https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb
wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.pb
Then convert from UShER pb format to Taxonium jsonl format:
usher_to_taxonium --input tfci.pb --output tfci-taxonium.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb \
--columns genbank_accession,country,date,pangolin_lineage
You can then open that tfci-taxonium.jsonl.gz
file at taxonium.org
Use Chronumental to infer a time tree
Taxonium tools can also use Chronumental to infer a time tree for the phylogeny.
pip install chronumental
usher_to_taxonium --input tfci.pb --output tfci-taxonium.jsonl.gz --metadata tfci.meta.tsv.gz --genbank hu1.gb \
--columns genbank_accession,country,date,pangolin_lineage --chronumental --chronumental_steps 300
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
taxoniumtools-2.0.90.tar.gz
(274.4 kB
view hashes)
Built Distribution
Close
Hashes for taxoniumtools-2.0.90-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3d83058bb3714a6c7eaa53e7bb04b79cabd05959d96855499b7cbae6a6fc52a3 |
|
MD5 | bce0e355414770ceaccf7f1ea3fa8b74 |
|
BLAKE2b-256 | b531103afe68d599c34fe7d3917c3a4a43140188247f0d12fee8645ef722d52d |