Pipeline components for real-time virus analysis

H7N9 build

How to run

1. Run all commands from this directory

2. Download FASTA files for all segments via fauna and prepare analysis

python avian.prepare.py

Running avian.prepare.py creates the files prepared/avian_ha.json, prepared/avian_na.json, etc...

3. Run builds

python avian.process.py --json prepared/avian_h7n9_ha.json
python avian.process.py --json prepared/avian_h7n9_na.json
python avian.process.py --json prepared/avian_h7n9_ns.json
python avian.process.py --json prepared/avian_h7n9_pb1.json
python avian.process.py --json prepared/avian_h7n9_pb2.json
python avian.process.py --json prepared/avian_h7n9_mp.json
python avian.process.py --json prepared/avian_h7n9_np.json
python avian.process.py --json prepared/avian_h7n9_pa.json

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

4. Copy JSONs to auspice

cp auspice/avian_* ../../../auspice/data/

5. Run auspice to visualize

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