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[phylo] Reconnect traits to export #252

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merged 5 commits into from
May 10, 2024
Merged

[phylo] Reconnect traits to export #252

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aafda78
phylo: use config params for traits params
joverlee521 May 9, 2024
5d42ca1
phylo: conditionalized traits input for rule export
joverlee521 May 9, 2024
7e95a16
phylo: restore disabling of geographic reconstruction
joverlee521 May 9, 2024
9bc91b8
phylo: replace hard-coded "results/" paths with `build_dir`
joverlee521 May 9, 2024
8a7eab4
phylo: Add traits to CI config
joverlee521 May 9, 2024
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4 changes: 4 additions & 0 deletions phylogenetic/build-configs/ci/config.yaml
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Expand Up @@ -77,6 +77,10 @@ clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

traits:
columns: ""
sampling_bias_correction: 3

## recency
recency: true

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4 changes: 4 additions & 0 deletions phylogenetic/defaults/hmpxv1/config.yaml
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Expand Up @@ -74,6 +74,10 @@ clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

traits:
columns: ""
sampling_bias_correction: 3

## recency
recency: true

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4 changes: 4 additions & 0 deletions phylogenetic/defaults/hmpxv1_big/config.yaml
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Expand Up @@ -50,6 +50,10 @@ clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

traits:
columns: ""
sampling_bias_correction: 3

## recency
recency: true

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4 changes: 4 additions & 0 deletions phylogenetic/defaults/mpxv/config.yaml
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Expand Up @@ -70,6 +70,10 @@ clock_rate: 3e-6
clock_std_dev: 6e-6
divergence_units: "mutations-per-site"

traits:
columns: ""
sampling_bias_correction: 3

## recency
recency: true

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4 changes: 2 additions & 2 deletions phylogenetic/rules/annotate_phylogeny.smk
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Expand Up @@ -72,8 +72,8 @@ rule traits:
output:
node_data=build_dir + "/{build_name}/traits.json",
params:
columns="country",
sampling_bias_correction=3,
columns=config["traits"]["columns"],
sampling_bias_correction=config["traits"]["sampling_bias_correction"],
strain_id=config["strain_id_field"],
shell:
"""
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16 changes: 10 additions & 6 deletions phylogenetic/rules/export.smk
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Expand Up @@ -32,9 +32,9 @@ OUTPUTS:

rule remove_time:
input:
"results/{build_name}/branch_lengths.json",
build_dir + "/{build_name}/branch_lengths.json",
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this is probably some snakemake lore i haven't absorbed yet, but i wonder: why concatenate instead of interpolate? (e.g., "{build_dir}/{build_name}/branch_lengths.json")

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Ah, this is using concatenation because the workflow uses a mix of variable (build_dir) and Snakemake wildcard (build_name) in the file paths.

We could update it to f"{build_dir}/{{build_name}}/branch_lengths.json" with double braces around build_name to keep the wildcard reference.

output:
"results/{build_name}/branch_lengths_no_time.json",
build_dir + "/{build_name}/branch_lengths_no_time.json",
shell:
"""
python3 scripts/remove_timeinfo.py --input-node-data {input} --output-node-data {output}
Expand Down Expand Up @@ -66,11 +66,15 @@ rule export:
tree=build_dir + "/{build_name}/tree.nwk",
metadata=build_dir + "/{build_name}/metadata.tsv",
branch_lengths=(
"results/{build_name}/branch_lengths.json"
build_dir + "/{build_name}/branch_lengths.json"
if config.get("timetree", False)
else "results/{build_name}/branch_lengths_no_time.json"
else build_dir + "/{build_name}/branch_lengths_no_time.json"
),
traits=(
build_dir + "/{build_name}/traits.json"
if config.get("traits", {}).get("columns", False)
else []
),
traits=build_dir + "/{build_name}/traits.json",
nt_muts=build_dir + "/{build_name}/nt_muts.json",
aa_muts=build_dir + "/{build_name}/aa_muts.json",
clades=build_dir + "/{build_name}/clades.json",
Expand All @@ -95,7 +99,7 @@ rule export:
--tree {input.tree} \
--metadata {input.metadata} \
--metadata-id-columns {params.strain_id} \
--node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.mutation_context} {input.clades} {input.recency}\
--node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} {input.mutation_context} {input.clades} {input.recency}\
--colors {input.colors} \
--lat-longs {input.lat_longs} \
--description {input.description} \
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