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get-data.sh
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#!/bin/bash
data_files=(
"manifest_guest.json" \
"dengue_all.json" "dengue_denv1.json" "dengue_denv2.json" "dengue_denv3.json" "dengue_denv4.json"\
"ebola.json" \
"ebola_2019-09-14-no-epi-id_meta.json" "ebola_2019-09-14-no-epi-id_tree.json" \
"lassa_s_tree.json" "lassa_s_meta.json" \
"lassa_l_tree.json" "lassa_l_meta.json" \
"measles.json" \
"mers_tree.json" "mers_meta.json" \
"mumps_global.json" "mumps_na.json" \
"WNV_NA_tree.json" "WNV_NA_meta.json" \
"zika.json" \
"flu_avian_h7n9_ha.json" \
"flu_avian_h7n9_mp.json" \
"flu_avian_h7n9_na.json" \
"flu_avian_h7n9_np.json" \
"flu_avian_h7n9_ns.json" \
"flu_avian_h7n9_pa.json" \
"flu_avian_h7n9_pb1.json" \
"flu_avian_h7n9_pb2.json" \
"flu_seasonal_h3n2_ha_2y.json" "flu_seasonal_h3n2_ha_2y_tip-frequencies.json" \
"flu_seasonal_h3n2_ha_3y.json" "flu_seasonal_h3n2_ha_3y_tip-frequencies.json" \
"flu_seasonal_h3n2_ha_6y.json" "flu_seasonal_h3n2_ha_6y_tip-frequencies.json" \
"flu_seasonal_h3n2_ha_12y.json" "flu_seasonal_h3n2_ha_12y_tip-frequencies.json" \
"flu_seasonal_h3n2_na_2y.json" "flu_seasonal_h3n2_na_2y_tip-frequencies.json" \
"flu_seasonal_h3n2_na_3y.json" "flu_seasonal_h3n2_na_3y_tip-frequencies.json" \
"flu_seasonal_h3n2_na_6y.json" "flu_seasonal_h3n2_na_6y_tip-frequencies.json" \
"flu_seasonal_h3n2_na_12y.json" "flu_seasonal_h3n2_na_12y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_ha_2y.json" "flu_seasonal_h1n1pdm_ha_2y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_ha_3y.json" "flu_seasonal_h1n1pdm_ha_3y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_ha_6y.json" "flu_seasonal_h1n1pdm_ha_6y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_ha_12y.json" "flu_seasonal_h1n1pdm_ha_12y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_ha_pandemic_meta.json" "flu_seasonal_h1n1pdm_ha_pandemic_tree.json" "flu_seasonal_h1n1pdm_ha_pandemic_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_na_2y.json" "flu_seasonal_h1n1pdm_na_2y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_na_3y.json" "flu_seasonal_h1n1pdm_na_3y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_na_6y.json" "flu_seasonal_h1n1pdm_na_6y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_na_12y.json" "flu_seasonal_h1n1pdm_na_12y_tip-frequencies.json" \
"flu_seasonal_h1n1pdm_na_pandemic_tree.json" "flu_seasonal_h1n1pdm_na_pandemic_meta.json" "flu_seasonal_h1n1pdm_na_pandemic_tip-frequencies.json" \
"flu_seasonal_vic_ha_2y.json" "flu_seasonal_vic_ha_2y_tip-frequencies.json" \
"flu_seasonal_vic_ha_3y.json" "flu_seasonal_vic_ha_3y_tip-frequencies.json" \
"flu_seasonal_vic_ha_6y.json" "flu_seasonal_vic_ha_6y_tip-frequencies.json" \
"flu_seasonal_vic_ha_12y.json" "flu_seasonal_vic_ha_12y_tip-frequencies.json" \
"flu_seasonal_vic_na_2y.json" "flu_seasonal_vic_na_2y_tip-frequencies.json" \
"flu_seasonal_vic_na_3y.json" "flu_seasonal_vic_na_3y_tip-frequencies.json" \
"flu_seasonal_vic_na_6y.json" "flu_seasonal_vic_na_6y_tip-frequencies.json" \
"flu_seasonal_vic_na_12y.json" "flu_seasonal_vic_na_12y_tip-frequencies.json" \
"flu_seasonal_yam_ha_2y.json" "flu_seasonal_yam_ha_2y_tip-frequencies.json" \
"flu_seasonal_yam_ha_3y.json" "flu_seasonal_yam_ha_3y_tip-frequencies.json" \
"flu_seasonal_yam_ha_6y.json" "flu_seasonal_yam_ha_6y_tip-frequencies.json" \
"flu_seasonal_yam_ha_12y.json" "flu_seasonal_yam_ha_12y_tip-frequencies.json" \
"flu_seasonal_yam_na_2y.json" "flu_seasonal_yam_na_2y_tip-frequencies.json" \
"flu_seasonal_yam_na_3y.json" "flu_seasonal_yam_na_3y_tip-frequencies.json" \
"flu_seasonal_yam_na_6y.json" "flu_seasonal_yam_na_6y_tip-frequencies.json" \
"flu_seasonal_yam_na_12y.json" "flu_seasonal_yam_na_12y_tip-frequencies.json" \
"tb_global_meta.json" "tb_global_tree.json" \
"enterovirus_d68_genome_meta.json" "enterovirus_d68_genome_tree.json" \
"enterovirus_d68_vp1_meta.json" "enterovirus_d68_vp1_tree.json" \
# The ncov datasets. It's not worth downloading them all, just grab the latest
"ncov_global.json" "ncov_africa.json" "ncov_oceania.json" "ncov_asia.json" \
"ncov_europe.json" "ncov_north-america.json" "ncov_south-america.json" \
"ncov_non-subsampled.json" \
# Adding the ncov datasets which are required by the narratives so they can be viewed locally
# (Note that these all include the date of upload in the filename)
"ncov_2020-01-23.json" "ncov_2020-01-25.json" "ncov_2020-01-26.json" "ncov_2020-01-30.json" \
"ncov_2020-03-04.json" "ncov_2020-03-05.json" "ncov_2020-03-11.json" "ncov_2020-03-13.json" \
"ncov_2020-03-20.json" "ncov_2020-03-27.json" "ncov_2020-04-03.json" \
"ncov_global_2020-04-09.json" "ncov_north-america_2020-04-17.json" \
)
rm -rf data/
mkdir -p data/
for i in "${data_files[@]}"
do
curl http://data.nextstrain.org/"${i}" --compressed -o data/"${i}"
done
echo "The local data directory ./data now contains up-to-date datasets from http://data.nextstrain.org"