jameshadfield/basel-flu

Input files

• data/nextstrain_tree_sub{x}.trees not committed to this repo
• data/location_mapping.csv not committed to this repo

Augur version

You must use augur branch beast-v2. When augur v6 is released these notes will be updated accordingly.

Convert lat-longs into auspice-usable format

This script uses ./data/location_mapping.csv and converts it into an augur-parseable format.

python scripts/make_lat_longs.py > results/lat_longs.tsv

Parse beast files using augur

numDate="2017.260" # 2017-04-05
for i in {1..10}; do
  augur import-beast --mcc data/nextstrain_tree_sub1.trees --output-tree results/basel-flu_${i}.new --output-node-data results/basel-flu_${i}_node_data.json --tip-date-format decimal --most-recent-tip-date ${numDate} --recursion-limit 10000;
done;

Modifications to the node-data specific to this analysis

for i in {1..10}; do
  python scripts/transform_node_data.py results/basel-flu_${i}_node_data.json results/basel-flu_${i}_node_data_transformed.json;
done

Export data for auspice

for i in {1..10}; do
  augur export v1 --tree results/basel-flu_${i}.new --node-data results/basel-flu_${i}_node_data_transformed.json --auspice-config config/auspice_config.json --output-meta auspice/basel-flu_${i}_meta.json --output-tree auspice/basel-flu_${i}_tree.json --metadata config/metadata.tsv --lat-longs results/lat_longs.tsv;
done