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|
Setup
$ source "$TESTDIR"/_setup.sh
Calculate diffusion-based tip frequencies from a refined tree.
$ ${AUGUR} frequencies \
> --method diffusion \
> --tree "$TESTDIR/../data/tree.nwk" \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --pivot-interval 3 \
> --output tip-frequencies.json > /dev/null
$ cat tip-frequencies.json
{
"BRA/2016/FC_6706": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"COL/FLR_00008/2015": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"Colombia/2016/ZC204Se": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"DOM/2016/BB_0183": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"EcEs062_16": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"HND/2016/HU_ME59": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"PAN/CDC_259359_V1_V3/2015": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"PRVABC59": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"VEN/UF_1/2016": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"ZKC2/2016": {
"global": [
0.1,
0.1,
0.1,
0.1
]
},
"counts": {
"global": [
0,
5,
5,
0
]
},
"generated_by": {
"program": "augur",
"version": ".*" (re)
},
"pivots": [
2015.7521,
2016.0041,
2016.2527,
2016.5014
]
} (no-eol)
|
