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Augur

Augur is Python package to forecast flu evolution. It will

  • import public sequence data
  • build a phylogenetic tree from this data
  • estimate clade fitnesses
  • estimate clade frequencies
  • project frequencies foreword

It is intended to be run in an always-on fashion, recomputing predictions daily and pushing predictions to a (static) website.

Build

To run locally, you'll need Firefox, Python, pip, muscle, RAxML, ruby and s3_website. With them installed, additional dependencies can be installed with:

pip install -r requirements.txt

Alternatively, you can run across platforms using Docker and the supplied Dockerfile

docker pull trvrb/augur
docker run -ti -e "GISAID_USER=$GISAID_USER" -e "GISAID_PASS=$GISAID_PASS" -e "S3_KEY=$S3_KEY" -e "S3_SECRET=$S3_SECRET" -e "S3_BUCKET=$S3_BUCKET" --privileged trvrb/augur /bin/bash

Before starting Python scripts, you'll need to run:

supervisord -c supervisord.conf

Run

Python scripts are run in the following run.py. This generates sequence and tree files, most notably site/tree.json. This file is uploaded to Amazon S3 by running upload.py.

Environment

You will need a GISAID account and an Amazon S3 account. Assumes environment variables:

  • GISAID_USER: GISAID user name
  • GISAID_PASS: GISAID password
  • S3_KEY: Amazon S3 key
  • S3_SECRET: Amazon S3 secret
  • S3_BUCKET: Amazon S3 bucket

Process

Ingest

Using Selenium and Python bindings to automate web crawling. GISAID requires login access. User credentials are stored in the ENV as GISAID_USER and GISAID_PASS.

Filter

Keeps viruses with full HA1 sequences, fully specified dates, cell passage and only one sequence per strain name.

Align

Align sequences with muscle and strip to just the 987 bases of HA1. This should take ~1.5 hours for ~15k sequences.

Frequencies

Estimate clade frequencies using SMC particle filtering.

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Owner
trvrb

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