Pipeline components for real-time virus analysis

Seasonal flu (H3N2, H1N1pdm, Vic, Yam) build

How to run

1. Run all commands from this directory

2. Download FASTA file via fauna and prepare analysis

python flu.prepare.py --lineage h3n2 --resolution 3y

Running this creates the file prepared/flu_seasonal_h3n2_ha_3y.json.

3. Run build

python flu.process.py --json prepared/flu_seasonal_h3n2_ha_3y.json

This creates intermediary files in processed/ and auspice-ready JSONs in auspice/.

4. Copy JSONs to auspice

cp auspice/flu_* ../../../auspice/data/

5. Run auspice to visualize

cd ../../../auspice
npm run start:local

How to run (batch)

The script run_flu.py will batch calls to flu.prepare.py and flu.process.py to run all combinations of lineage (h3n2, h1n1pdm, vic, yam) and resolution (2y, 3y, 6y, 12y). python run_flu.py

Summary of the necessary files

flu.prepare.pyPrepare script.
flu.process.pyProcess script.
flu_info.pyHolds (a lot of) information about sequences to drop, reference genomes etc. Used by prepare.
../../fauna/data/<LINEAGE>_<SEG>.fasta(Fauna) fasta file
colors.flu.tsvcolor maps