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Use gene reference files to generate E gene trees #48

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merged 8 commits into from
May 13, 2024
Merged

Use gene reference files to generate E gene trees #48

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81eeef9
prepare sequences
j23414 May 10, 2024
cba737f
annotate phylogeny
j23414 May 10, 2024
e591a0b
Add E gene targets
j23414 May 10, 2024
1e48186
Set E tree default color to Nextclade genotype
j23414 May 10, 2024
0cbdeb8
fixup: denv2 genotype ordering to match clade_membership
j23414 May 10, 2024
040d344
E gene builds exclude the augur clades call
j23414 May 10, 2024
b827c09
Add NCBI serotypes annotations to the phylogeny
j23414 May 10, 2024
6423792
fixup: change default display to rooted time-tree
j23414 May 11, 2024
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2 changes: 1 addition & 1 deletion phylogenetic/rules/export.smk
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Expand Up @@ -42,7 +42,7 @@ rule prepare_auspice_config:
output:
auspice_config="results/config/{gene}/auspice_config_{serotype}.json",
params:
replace_clade_key="clade_membership",
replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"nextclade_subtype",
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Because the clade_membership is automatically used to create the clade branch label in augur export, this change means the E gene build will not have the automatic clade branch label.

It's possible to create custom branch labels since nextstrain/augur#728, but this uses augur clades to create the labels and the workflow is skipping augur clades for the E gene build 😅

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Since the nextclade_subtype field is being added through augur traits, maybe augur traits should be updated to support adding branch labels as well...

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Good to know! I'm currently planning to explore serotype and genotype-defining E mutations (which would create clade_membership for E gene builds) in a future PR.

But if that doesn't work out, I'll explore "create custom branch labels ..." route you've referenced.

replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"DENV genotype",
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To mirror the title NCBI serotype added below, maybe the default clade_membership title should be updated to Nextstrain serotype?

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Thank you for flagging! I'm considering renaming NCBI serotype toSerotype (NCBI) to better match naming convention used in measle's Genotype (NCBI) title. Then, I agree that the default title for clade_membership should be renamed from Serotype to Serotype (Nextstrain).

To recap:

  • NCBI serotype -> Serotype (NCBI): indicating that denv1-4 assignment is based on NCBI GenBank record annotation
  • Serotype -> Serotype (Nextstrain): indicating that denv1-4 assignment is based on augur clades call using full-genome-level-serotype-defining amino acid mutations
  • Nextclade genotype -> Genotype (Nextclade): indicating genotype level assignment within the serotype (e.g. DENV1/S) based on Nextclade call

This naming adjustment leaves space for a potential Genotype (NCBI) if we develop a script for parsing genotype annotations from the GenBank data.

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Ah, actually I think I'll merge this pull request as it is, and handle the renaming mentioned above in a later PR. That way, we can address it along with fixing this issue: #41.

run:
data = {
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