Skip to main content

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

For more information see the docs

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-2.0.223.tar.gz (275.3 kB view details)

Uploaded Source

Built Distribution

taxoniumtools-2.0.223-py3-none-any.whl (19.8 kB view details)

Uploaded Python 3

File details

Details for the file taxoniumtools-2.0.223.tar.gz.

File metadata

  • Download URL: taxoniumtools-2.0.223.tar.gz
  • Upload date:
  • Size: 275.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.9.20

File hashes

Hashes for taxoniumtools-2.0.223.tar.gz
Algorithm Hash digest
SHA256 37d2fc3d1871a95ffad9a6f1bd7bc68c2000577b60d98ec053bce09f7f8580bf
MD5 68175956d76aca525633f7c3abc4fd17
BLAKE2b-256 195cf340430bfad69988db15248803d770e7dca1980f3014aad7994519cfc9bb

See more details on using hashes here.

File details

Details for the file taxoniumtools-2.0.223-py3-none-any.whl.

File metadata

File hashes

Hashes for taxoniumtools-2.0.223-py3-none-any.whl
Algorithm Hash digest
SHA256 173a5717d8f9792a8c403a06bf6e67c8c64a657d4e92d6dd50b26049c976ac95
MD5 54744c462ef37282e21b5d165838ef0a
BLAKE2b-256 a9930b29b68d9daeefdf6f1c70899b0d34344b098a11003b4d03830f06c661d6

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page