Merge pull request #13 from nextstrain/relabel-clades-12

Relabel clades numerically, rather than geographically [#12]

nextclade/README.md

@@ -1,7 +1,7 @@
 # Yellow Fever Virus Nextclade Dataset Tree
 
 This workflow creates a phylogenetic tree that can be used as part of
-a Nextclade dataset to assign genotypes to yellow fever virus samples
+a Nextclade dataset to assign clades to yellow fever virus samples
 based on [Mutebi et al.][] (J Virol. 2001 Aug;75(15):6999-7008) and
 [Bryant et al.][] (PLoS Pathog. 2007 May 18;3(5):e75).
 
@@ -14,6 +14,22 @@ based on [Mutebi et al.][] (J Virol. 2001 Aug;75(15):6999-7008) and
 * Provide the following coloring options on the tree:
   * Genotype assignment from `augur clades`
 
+The clades we annotate (Clade I-VII) are roughly equivalent with the
+following genotypes as described in the aforementioned two papers:
+
+| Clade     | Genotype            |
+|-----------|---------------------|
+| Clade I   | Angola              |
+| Clade II  | East Africa         |
+| Clade III | East Central/Africa |
+| Clade IV  | West Africa I       |
+| Clade V   | West Africa II      |
+| Clade VI  | South America I     |
+| Clade VII | South America II    |
+
+(N.b., this table is available as a TSV in this repo, at
+`nextclade/defaults/clade-to-genotype.tsv`.)
+
 ## How to create a new tree
 
 * Run the workflow: `nextstrain build .`

nextclade/defaults/clade-to-genotype.tsv

@@ -0,0 +1,8 @@
+Clade	Genotype
+Clade I	Angola
+Clade II	East Africa
+Clade III	East Central/Africa
+Clade IV	West Africa I
+Clade V	West Africa II
+Clade VI	South America I
+Clade VII	South America II

nextclade/defaults/clades.tsv

@@ -1,40 +1,40 @@
 clade	gene	site	alt
-Angola	nuc	111	G
-Angola	nuc	219	T
-Angola	nuc	240	C
-Angola	nuc	246	A
-Angola	nuc	252	A
-Angola	nuc	255	A
-Angola	nuc	291	G
-Angola	nuc	294	A
-Angola	nuc	300	A
-Angola	nuc	315	G
-Angola	nuc	327	G
-Angola	nuc	372	A
-Angola	nuc	420	A
-Angola	nuc	432	A
-Angola	nuc	453	T
-Angola	nuc	492	G
-Angola	nuc	651	T
-Angola	nuc	72	A
-Angola	nuc	81	G
-Angola	nuc	88	C
-Angola	nuc	90	A
-Angola	nuc	99	T
-East Africa	nuc	171	G
-East Africa	nuc	438	G
-East Africa	nuc	45	A
-East Africa	nuc	468	T
-East/Central Africa	nuc	228	G
-South America I	nuc	219	A
-South America I	nuc	532	A
-South America II	nuc	114	C
-South America II	nuc	193	T
-South America II	nuc	249	A
-South America II	nuc	639	G
-West Africa I	nuc	183	G
-West Africa I	nuc	255	C
-West Africa II	nuc	270	A
-West Africa II	nuc	321	T
-West Africa II	nuc	477 	A
-West Africa II	nuc	93	T
+Clade I	nuc	111	G
+Clade I	nuc	219	T
+Clade I	nuc	240	C
+Clade I	nuc	246	A
+Clade I	nuc	252	A
+Clade I	nuc	255	A
+Clade I	nuc	291	G
+Clade I	nuc	294	A
+Clade I	nuc	300	A
+Clade I	nuc	315	G
+Clade I	nuc	327	G
+Clade I	nuc	372	A
+Clade I	nuc	420	A
+Clade I	nuc	432	A
+Clade I	nuc	453	T
+Clade I	nuc	492	G
+Clade I	nuc	651	T
+Clade I	nuc	72	A
+Clade I	nuc	81	G
+Clade I	nuc	88	C
+Clade I	nuc	90	A
+Clade I	nuc	99	T
+Clade II	nuc	171	G
+Clade II	nuc	438	G
+Clade II	nuc	45	A
+Clade II	nuc	468	T
+Clade III	nuc	228	G
+Clade VI	nuc	219	A
+Clade VI	nuc	532	A
+Clade VII	nuc	114	C
+Clade VII	nuc	193	T
+Clade VII	nuc	249	A
+Clade VII	nuc	639	G
+Clade IV	nuc	183	G
+Clade IV	nuc	255	C
+Clade V	nuc	270	A
+Clade V	nuc	321	T
+Clade V	nuc	477 	A
+Clade V	nuc	93	T

nextclade/defaults/colors.tsv

@@ -1,8 +1,8 @@
 # genotypes assigned by augur clades
-clade_membership	Angola	#3F63CF
-clade_membership	East Africa	#529AB6
-clade_membership	East/Central Africa	#75B681
-clade_membership	South America I	#A6BE55
-clade_membership	South America II	#D4B13F
-clade_membership	West Africa I	#E68133
-clade_membership	West Africa II	#DC2F24
+clade_membership	Clade I	#3F63CF
+clade_membership	Clade II	#529AB6
+clade_membership	Clade III	#75B681
+clade_membership	Clade IV	#A6BE55
+clade_membership	Clade V	#DC2F24
+clade_membership	Clade VI	#E68133
+clade_membership	Clade VII	#D4B13F

nextclade/defaults/nextclade-dataset/README.md

@@ -10,7 +10,7 @@
 
 ## Scope of this dataset
 
-This dataset assigns genotypes to yellow fever virus samples based on
+This dataset assigns clades to yellow fever virus samples based on
 strain and genotype information from [Mutebi et al.][] (J Virol. 2001
 Aug;75(15):6999-7008) and [Bryant et al.][] (PLoS Pathog. 2007 May 18;3(5):e75)
 
@@ -21,6 +21,19 @@ comprises the 3' end of the pre-membrane protein (prM) gene, the
 entire membrane protein (M) gene, and the 5' end of the envelope
 protein (E) gene.
 
+The clades we annotate (Clade I-VII) are roughly equivalent with the
+following genotypes as described in the aforementioned two papers:
+
+| Clade     | Genotype            |
+|-----------|---------------------|
+| Clade I   | Angola              |
+| Clade II  | East Africa         |
+| Clade III | East Central/Africa |
+| Clade IV  | West Africa I       |
+| Clade V   | West Africa II      |
+| Clade VI  | South America I     |
+| Clade VII | South America II    |
+
 (N.b., the reference sequence used in this data set is actually 672nt
 long, from bases 641-1312 of the genome reference. The 2 extra bases
 make the reference an complete open reading frame.)