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Make tree for 450bp of the N gene ("N450") #20

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Merged
kimandrews merged 11 commits into from
Apr 1, 2024
Merged

Make tree for 450bp of the N gene ("N450") #20

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55ea0ce
Add reference files for N450 region
kimandrews Mar 21, 2024
edbefd5
Prepare N450 sequences for phylogenetic analysis
kimandrews Mar 21, 2024
8343876
Construct phylogeny for N450 region
kimandrews Mar 21, 2024
d55342b
Annotate phylogeny for N450 region
kimandrews Mar 21, 2024
ab92a1b
Export phylogeny for N450 region
kimandrews Mar 21, 2024
f39ba8b
Use `--stochastic-resolve` option for `augur refine`
kimandrews Mar 28, 2024
119fbcf
Remove "country" colors from `defaults/colors.tsv`
kimandrews Mar 28, 2024
862dbaf
Change default display to rooted time-tree
kimandrews Mar 28, 2024
8bea320
Use `--metadata-columns` to export "author" in auspice_config.json
kimandrews Mar 28, 2024
a9d2644
Organize builds as directories within `results`
kimandrews Mar 28, 2024
bf83a42
Update Changelog
kimandrews Apr 1, 2024
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2 changes: 1 addition & 1 deletion phylogenetic/Snakefile
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Expand Up @@ -4,7 +4,7 @@ configfile: "defaults/config.yaml"

rule all:
input:
auspice_json = "auspice/measles.json",
auspice_json = expand("auspice/measles_{gene}.json", gene=genes)

include: "rules/prepare_sequences.smk"
include: "rules/prepare_sequences_N450.smk"
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49 changes: 49 additions & 0 deletions phylogenetic/defaults/auspice_config_N450.json
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@@ -0,0 +1,49 @@
{
"title": "Real-time tracking of measles virus evolution",
"maintainers": [
{"name": "Kim Andrews", "url": "https://bedford.io/team/kim-andrews/"},
{"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}
],
"build_url": "https://github.com/nextstrain/measles",
"colorings": [
{
"key": "gt",
"title": "Genotype",
"type": "categorical"
},
{
"key": "num_date",
"title": "Date",
"type": "continuous"
},
{
"key": "author",
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@jameshadfield jameshadfield Mar 25, 2024 •
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[Not blocking this PR]

We used to add "author" as a color-by as a workaround so that it appeared as a filtering option in Auspice, however a couple of recent changes have rendered this pattern unnecessary. We can now use "metadata_columns" in the auspice-config JSON (or --metadata-columns) to export "author" and Auspice will automatically add it as a filtering option. This is nicer than exposing author as a coloring.

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@kimandrews kimandrews Mar 28, 2024

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Done in 8bea320

"title": "Author",
"type": "categorical"
},
{
"key": "country",
"title": "Country",
"type": "categorical"
},
{
"key": "region",
"title": "Region",
"type": "categorical"
}
],
"geo_resolutions": [
"country",
"region"
],
"display_defaults": {
"map_triplicate": true,
"distance_measure": "div",
"layout": "unrooted"
},
"filters": [
"country",
"region",
"author"
]
}
1 change: 1 addition & 0 deletions phylogenetic/defaults/config.yaml
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Expand Up @@ -6,6 +6,7 @@ files:
reference_N450_fasta: "defaults/measles_reference_N450.fasta"
colors: "defaults/colors.tsv"
auspice_config: "defaults/auspice_config.json"
auspice_config_N450: "defaults/auspice_config_N450.json"
filter:
group_by: "country year month"
sequences_per_group: 20
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14 changes: 8 additions & 6 deletions phylogenetic/rules/export.smk
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Expand Up @@ -8,15 +8,17 @@ See Augur's usage docs for these commands for more details.
rule export:
"""Exporting data files for for auspice"""
input:
tree = "results/tree.nwk",
tree = "results/tree_{gene}.nwk",
metadata = "data/metadata.tsv",
branch_lengths = "results/branch_lengths.json",
nt_muts = "results/nt_muts.json",
aa_muts = "results/aa_muts.json",
branch_lengths = "results/branch_lengths_{gene}.json",
nt_muts = "results/nt_muts_{gene}.json",
aa_muts = "results/aa_muts_{gene}.json",
colors = config["files"]["colors"],
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@jameshadfield jameshadfield Mar 25, 2024

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I'd suggest removing all the "country" colours from the defaults/colors.tsv in this PR simply because a number of countries are missing colours. Auspice will pick a better set of colours than the current situation of some colours + some greys. We can then add nicer colours in a subsequent PR, as desired.

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@kimandrews kimandrews Mar 28, 2024

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Done in 119fbcf

auspice_config = config["files"]["auspice_config"]
auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json"

output:
auspice_json = rules.all.input.auspice_json
auspice_json = "auspice/measles_{gene}.json",
root_sequence = "auspice/measles_{gene}_root-sequence.json"
params:
strain_id = config["strain_id_field"]
shell:
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