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Include vaccine strains #23

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merged 4 commits into from
Apr 16, 2024
Merged

Include vaccine strains #23

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6f1f2e2
Include strain and date annotations for sequenced vaccine strains
trvrb Apr 12, 2024
4770a7d
Switch to country / year subsampling for genome build
trvrb Apr 12, 2024
796f747
Include "strain name" as coloring
trvrb Apr 12, 2024
b51ea60
Export strain, division and location as additional metadata
trvrb Apr 12, 2024
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20 changes: 20 additions & 0 deletions ingest/defaults/annotations.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,23 @@
# If there are multiple annotations for the same id and field, then the last value is used
# Lines starting with '#' are treated as comments
# Any '#' after the field value are treated as comments.
#
# Vaccine strain information from Parks et al. Comparison of predicted amino acid
# sequences of measles virus strains in the Edmonston vaccine lineage
# https://doi.org/10.1128/jvi.75.2.910-920.2001
AF266288.2 strain Measles strain Edmonston WT
AF266288.2 date 1954
AF266288.2 region North America
AF266288.2 country USA
AF266288.2 division Massachusetts
AF266288.2 location Boston
AF266287.1 strain Measles vaccine strain Moraten
AF266287.1 date 1954
AF266290.1 strain Measles vaccine strain Zagreb
AF266290.1 date 1954
AF266289.1 strain Measles vaccine strain Rubeovax
AF266289.1 date 1954
AF266291.1 strain Measles vaccine strain Schwarz
AF266291.1 date 1954
AF266286.1 strain Measles vaccine strain AIK-C
AF266286.1 date 1954
8 changes: 5 additions & 3 deletions phylogenetic/defaults/config.yaml
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Expand Up @@ -7,8 +7,8 @@ files:
colors: "defaults/colors.tsv"
auspice_config: "defaults/auspice_config.json"
auspice_config_N450: "defaults/auspice_config_N450.json"
filter:
group_by: "country year month"
filter:
group_by: "country year"
sequences_per_group: 20
min_date: 1950
min_length: 5000
Expand All @@ -20,6 +20,8 @@ filter_N450:
refine:
coalescent: "opt"
date_inference: "marginal"
clock_filter_iqd: 4
clock_filter_iqd: 4
ancestral:
inference: "joint"
export:
metadata_columns: "strain division location"
Comment on lines +26 to +27
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@kimandrews kimandrews Apr 12, 2024 •
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That sounds good to surface the strain names now. Eventually we should be able to pull more strain names from GenBank, after NCBI Datasets starts pulling the "strain" field, which is where most measles strain names are reported on GenBank (currently we are getting strain names from Genbank's "isolate" field, which NCBI Datasets does pull). NCBI says this is planned for sometime this year. This would also enable us to recover dates for some samples that have empty dates, since dates are part of the strain name.

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Excellent! Thanks for the context.

6 changes: 3 additions & 3 deletions phylogenetic/rules/export.smk
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Expand Up @@ -15,12 +15,12 @@ rule export:
aa_muts = "results/{gene}/aa_muts.json",
colors = config["files"]["colors"],
auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json"

output:
auspice_json = "auspice/measles_{gene}.json",
root_sequence = "auspice/measles_{gene}_root-sequence.json"
params:
strain_id = config["strain_id_field"]
strain_id = config["strain_id_field"],
metadata_columns = config["export"]["metadata_columns"]
shell:
"""
augur export v2 \
Expand All @@ -29,8 +29,8 @@ rule export:
--metadata-id-columns {params.strain_id} \
--node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \
--colors {input.colors} \
--metadata-columns {params.metadata_columns} \
--auspice-config {input.auspice_config} \
--include-root-sequence \
--output {output.auspice_json}
"""