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Add display name clades_display_name.tsv for human friendly names #1050

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Add display name clades_display_name.tsv for human friendly names #1050

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6860e1b
Add clades_display_name.tsv
corneliusroemer Mar 16, 2023
07ac3c4
Use clades_display_name.tsv as default & in color_ordering.tsv
corneliusroemer Mar 17, 2023
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176 changes: 176 additions & 0 deletions defaults/clades_display_name.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,176 @@
clade gene site alt

19A nuc 8782 C
19A nuc 14408 C

19B nuc 8782 T
19B nuc 28144 C

20A clade 19A
20A nuc 14408 T
20A nuc 23403 G

20B clade 20A
20B nuc 28881 A
20B nuc 28882 A

20C clade 20A
20C nuc 1059 T
20C nuc 25563 T

20D clade 20B
20D nuc 4002 T
20D nuc 10097 A
20D nuc 13536 T
20D nuc 23731 T

20E clade 20A
20E nuc 22227 T
20E nuc 28932 T
20E nuc 29645 T

20F clade 20B
20F nuc 1163 T
20F nuc 7540 C
20F nuc 16647 T
20F nuc 18555 T
20F nuc 22992 A
20F nuc 23401 A

20G clade 20C
20G nuc 10319 T
20G nuc 18424 G
20G nuc 25907 T
20G nuc 27964 T
20G nuc 28472 T
20G nuc 28869 T

20H (Beta) clade 20C
20H (Beta) nuc 23012 A
20H (Beta) nuc 23063 T
20H (Beta) nuc 23403 G
20H (Beta) nuc 26456 T

20I (Alpha) clade 20B
20I (Alpha) nuc 14676 T
20I (Alpha) nuc 15279 T
20I (Alpha) nuc 23063 T

20J (Gamma) clade 20B
20J (Gamma) nuc 733 C
20J (Gamma) nuc 2749 T
20J (Gamma) nuc 3828 T
20J (Gamma) nuc 5648 C
20J (Gamma) nuc 12778 T
20J (Gamma) nuc 13860 T

21A (Delta) clade 20A
21A (Delta) nuc 21618 G
21A (Delta) nuc 26767 C
21A (Delta) nuc 28461 G

21B (Kappa) clade 20A
21B (Kappa) nuc 17523 T
21B (Kappa) nuc 22917 G
21B (Kappa) nuc 23012 C
21B (Kappa) nuc 27638 C
21B (Kappa) nuc 28881 T
21B (Kappa) nuc 29402 T

21C (Epsilon) clade 20C
21C (Epsilon) nuc 17014 T
21C (Epsilon) nuc 21600 T
21C (Epsilon) nuc 22018 T
21C (Epsilon) nuc 22917 G

21D (Eta) clade 20A
21D (Eta) nuc 14407 T
21D (Eta) nuc 20724 G
21D (Eta) nuc 23593 C
21D (Eta) nuc 24224 C
21D (Eta) nuc 24748 T

21E (Theta) clade 20B
21E (Theta) nuc 12049 T
21E (Theta) nuc 23341 C
21E (Theta) nuc 23604 A
21E (Theta) nuc 24187 A
21E (Theta) nuc 24836 A

21F (Iota) clade 20C
21F (Iota) nuc 16500 C
21F (Iota) nuc 20262 G
21F (Iota) nuc 21575 T
21F (Iota) nuc 22320 G

21G (Lambda) clade 20D
21G (Lambda) nuc 21786 T
21G (Lambda) nuc 21789 T
21G (Lambda) nuc 22917 A
21G (Lambda) nuc 23031 C

21H (Mu) clade 20A
21H (Mu) nuc 3428 G
21H (Mu) nuc 4878 T
21H (Mu) nuc 11451 G
21H (Mu) nuc 13057 T
21H (Mu) nuc 17491 T
21H (Mu) nuc 27925 A

21I (Delta) clade 21A (Delta)
21I (Delta) nuc 5184 T
21I (Delta) nuc 9891 T
21I (Delta) nuc 22227 T

21J (Delta) clade 21A (Delta)
21J (Delta) nuc 11332 G
21J (Delta) nuc 19220 T

21K (BA.1) clade 21M (Omicron)
21K (BA.1) nuc 15240 T
21K (BA.1) nuc 23202 A
21K (BA.1) nuc 23525 T
21K (BA.1) nuc 27259 C

21L (BA.2) clade 21M (Omicron)
21L (BA.2) nuc 21618 T
21L (BA.2) nuc 22775 A

21M (Omicron) clade 20B
21M (Omicron) nuc 18163 G
21M (Omicron) nuc 23599 G

22A (BA.4) clade 21L (BA.2)
22A (BA.4) nuc 12160 A
22A (BA.4) nuc 9866 C
22A (BA.4) nuc 28724 T

22B (BA.5) clade 21L (BA.2)
22B (BA.5) nuc 12160 A
22B (BA.5) nuc 9866 C
22B (BA.5) nuc 27259 A

22C (BA.2.12.1) clade 21L (BA.2)
22C (BA.2.12.1) nuc 22917 A
22C (BA.2.12.1) nuc 23673 T

22D (BA.2.75) clade 21L (BA.2)
22D (BA.2.75) nuc 3796 T
22D (BA.2.75) nuc 26275 G

22E (BQ.1) clade 22B (BA.5)
22E (BQ.1) nuc 14257 C
22E (BQ.1) nuc 16935 A
22E (BQ.1) nuc 28312 T
22E (BQ.1) nuc 22942 A

22F (XBB) clade 21L (BA.2)
22F (XBB) nuc 15461 A
22F (XBB) nuc 17859 C
22F (XBB) nuc 23019 C
22F (XBB) nuc 26275 G

23A (XBB.1.5) clade 22F (XBB)
23A (XBB.1.5) nuc 22317 T
23A (XBB.1.5) nuc 23018 C
23A (XBB.1.5) nuc 27915 T
24 changes: 12 additions & 12 deletions defaults/color_ordering.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -33525,9 +33525,9 @@ recency New
################


clade_membership 20H (Beta, V2)
clade_membership 20I (Alpha, V1)
clade_membership 20J (Gamma, V3)
clade_membership 20H (Beta)
clade_membership 20I (Alpha)
clade_membership 20J (Gamma)
clade_membership 21A (Delta)
clade_membership 21I (Delta)
clade_membership 21J (Delta)
Expand All @@ -33538,16 +33538,16 @@ clade_membership 21E (Theta)
clade_membership 21F (Iota)
clade_membership 21G (Lambda)
clade_membership 21H (Mu)
clade_membership 21K (Omicron)
clade_membership 21L (Omicron)
clade_membership 21M (Omicron)
clade_membership 22A (Omicron)
clade_membership 22B (Omicron)
clade_membership 22C (Omicron)
clade_membership 22D (Omicron)
clade_membership 22E (Omicron)
clade_membership 22F (Omicron)
clade_membership 23A (Omicron)
clade_membership 21K (BA.1)
clade_membership 21L (BA.2)
clade_membership 22A (BA.4)
clade_membership 22B (BA.5)
clade_membership 22C (BA.2.12.1)
clade_membership 22D (BA.2.75)
clade_membership 22E (BQ.1)
clade_membership 22F (XBB)
clade_membership 23A (XBB.1.5)

################

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2 changes: 1 addition & 1 deletion defaults/parameters.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ files:
auspice_config: "defaults/auspice_config.json"
lat_longs: "defaults/lat_longs.tsv"
description: "defaults/description.md"
clades: "defaults/clades.tsv"
clades: "defaults/clades_display_name.tsv"
emerging_lineages: "defaults/emerging_lineages.tsv"
mutational_fitness_distance_map: "defaults/mutational_fitness_distance_map.json"
sites_to_mask: "defaults/sites_ignored_for_tree_topology.txt"
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