Metadata-Version: 2.1
Name: taxoniumtools
Version: 2.0.18
Summary: Generate files for taxonium
Home-page: https://github.com/theosanderson/taxonium
Author: Theo Sanderson
Author-email: theo@theo.io
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/theosanderson/taxonium/issues
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: treeswift
Requires-Dist: alive-progress
Requires-Dist: biopython
Requires-Dist: pandas
Requires-Dist: google-api-python-client

# Taxonium tools

Taxonium tools is a Python utility that allows you to generate Taxonium format files from [UShER](https://usher-wiki.readthedocs.io/en/latest/) 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
```

```
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](http://taxonium.org)

### Use Chronumental to infer a time tree

Taxonium tools can also use [Chronumental](https://github.com/theosanderson/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
```


