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Separate clade definitions and lineage definitions #71

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Separate clade definitions and lineage definitions #71

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5 changes: 5 additions & 0 deletions config/auspice_config_hmpxv1.json
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,11 @@
],
"build_url": "https://github.com/nextstrain/monkeypox",
"colorings": [
{
"key": "clade_membership",
"title": "Lineage",
"type": "categorical"
},
{
"key": "outbreak_associated",
"title": "Outbreak Associated",
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16 changes: 2 additions & 14 deletions config/clades.tsv → config/clades_mpxv.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,5 @@ MPXV Clade 3 nuc 150979 A
MPXV Clade 3 nuc 35361 C
MPXV Clade 3 nuc 48157 C

hMPXV-1 A clade MPXV Clade 3
hMPXV-1 A nuc 48536 A

A.2 clade hMPXV-1 A
A.2 nuc 34481 T

A.1 clade hMPXV-1 A
A.1 nuc 83335 T

A.1.1 clade A.1
A.1.1 nuc 34468 A

B.1 clade A.1.1
B.1 nuc 77392 A
hMPXV-1 clade MPXV Clade 3
hMPXV-1 nuc 48536 A
2 changes: 1 addition & 1 deletion config/config_hmpxv1.yaml
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Expand Up @@ -3,7 +3,7 @@ reference: "config/reference.fasta"
genemap: "config/genemap.gff"
genbank_reference: "config/reference.gb"
colors: "config/colors.tsv"
clades: "config/clades.tsv"
clades: "config/lineages_hmpxv1.tsv"
lat_longs: "config/lat_longs.tsv"
auspice_config: "config/auspice_config_hmpxv1.json"
description: "config/description.md"
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2 changes: 1 addition & 1 deletion config/config_mpxv.yaml
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Expand Up @@ -6,7 +6,7 @@ colors: "config/colors.tsv"
lat_longs: "config/lat_longs.tsv"
auspice_config: "config/auspice_config_mpxv.json"
description: "config/description.md"
clades: "config/clades.tsv"
clades: "config/clades_mpxv.tsv"

strain_id_field: "accession"
display_strain_field: "strain_original"
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20 changes: 20 additions & 0 deletions config/lineages_hmpxv1.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
clade gene site alt
MPXV Clade 3 nuc 86511 G
MPXV Clade 3 nuc 150979 A
MPXV Clade 3 nuc 35361 C
MPXV Clade 3 nuc 48157 C

A clade MPXV Clade 3
A nuc 48536 A

A.2 clade A
A.2 nuc 34481 T

A.1 clade A
A.1 nuc 83335 T

A.1.1 clade A.1
A.1.1 nuc 34468 A

B.1 clade A.1.1
B.1 nuc 77392 A