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Filter cattle-outbreak using GenoFLU B3.13 #140

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Feb 24, 2025
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Filter cattle-outbreak using GenoFLU B3.13 #140

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5 changes: 4 additions & 1 deletion Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -64,18 +64,21 @@ files = rules.files.params

def subtypes_by_subtype_wildcard(wildcards):

# TODO - this function does more than strictly subtype filtering as certain builds filter to
# GenoFLU constellation, and in the future this may be expanded. We should rename the function!
# TODO XXX - move to configs (started in https://github.com/nextstrain/avian-flu/pull/104 but
# We should make the entire query config-definable)
if wildcards.subtype == 'h5n1-d1.1':
return "genoflu in 'D1.1'"
elif wildcards.subtype == 'h5n1-cattle-outbreak':
return "genoflu in 'B3.13'"

db = {
'h5nx': ['h5n1', 'h5n2', 'h5n3', 'h5n4', 'h5n5', 'h5n6', 'h5n7', 'h5n8', 'h5n9'],
'h5n1': ['h5n1'],
'h7n9': ['h7n9'],
'h9n2': ['h9n2'],
}
db['h5n1-cattle-outbreak'] = [*db['h5nx']]
assert wildcards.subtype in db, (f"Subtype {wildcards.subtype!r} is not defined in the snakemake function "
"`subtypes_by_subtype_wildcard` -- is there a typo in the subtype you are targetting?")
return(f"subtype in [{', '.join([repr(s) for s in db[wildcards.subtype]])}]")
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5 changes: 5 additions & 0 deletions config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json
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Expand Up @@ -79,6 +79,11 @@
"title": "Subtype",
"type": "categorical"
},
{
"key": "genoflu",
"title": "GenoFLU constellation",
"type": "categorical"
},
{
"key": "h5_label_clade",
"title": "Provisional LABEL Clade",
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31 changes: 4 additions & 27 deletions config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt
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Expand Up @@ -9,6 +9,10 @@ A/Cattle/USA/24-009027-002-v/2024 # Duplicate of A/cattle/Michigan/24-009027-002
A/PEFA/USA/24-005915-001-original/2024 # Duplicate of A/Peregrinefalcon/California/24-005915-001/2024
A/Skunk/USA/24-006483-001-original/2024 # Duplicate of A/skunk/NewMexico/24-006483-001/2024

# Many of the following exclude strains were added prior to filtering on GenoFLU
# constellation B3.13 and thus may not be applicable any more. We can clean these up
# in the future if desired.

# Dropping these strains from include due to excess private mutations
A/cattle/NorthCarolina/24-010327-002/2024
A/cattle/Texas/24-009495-007/2024
Expand Down Expand Up @@ -246,30 +250,3 @@ A/westerngull/California/24-004708-001/2024
A/WesternGull/USA/24-004708-001-original/2024
A/WesternSandpiper/USA/24-004707-001-original/2024
A/woodduck/NorthCarolina/W24-026/2024

# D1.1 spillover
A/StripedSkunk/WA/W240530074-2-1/2024
A/CATTLE/USA/25-002645-006/2025
A/CATTLE/USA/25-002645-005/2025
A/CATTLE/USA/25-002645-004/2025
A/CATTLE/USA/25-002645-003/2025
A/chicken/AR/24-037983-003-original/2024
A/chicken/AR/24-037983-001-original/2024
A/chicken/AR/24-037983-002-original/2024
A/chicken/MN/24-038159-002-original/2024
A/Duck/MN/24-038159-001-original/2024
A/goose/MN/24-038159-004-original/2024
A/Turkey/MN/24-035355-002-original/2024
A/Turkey/MN/24-035355-001-original/2024
A/Turkey/MN/24-035521-001-original/2024
A/Turkey/MN/24-035524-003-original/2024
A/Turkey/MN/24-035524-004-original/2024
A/Turkey/MN/24-035524-001-original/2024
A/Turkey/MN/24-035524-002-original/2024
A/Turkey/MN/24-034932-001-original/2024
A/Turkey/MN/24-034932-003-original/2024
A/Turkey/MN/24-034932-002-original/2024
A/Turkey/MN/24-035355-003-original/2024
A/Turkey/MN/24-036792-002-original/2024
A/Turkey/MN/24-036792-003-original/2024
A/Turkey/MN/24-036792-001-original/2024
5 changes: 0 additions & 5 deletions rules/cattle-flu.smk
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Expand Up @@ -14,9 +14,6 @@ rule filter_segments_for_genome:
exclude = config['dropped_strains'],
output:
sequences = "results/{subtype}/{segment}/{time}/filtered_{genome_seg}.fasta"
params:
min_date = "2024-01-01",
query = 'region == "North America"'
wildcard_constraints:
subtype = 'h5n1-cattle-outbreak|h5n1-d1.1',
segment = 'genome',
Expand All @@ -29,8 +26,6 @@ rule filter_segments_for_genome:
--metadata {input.metadata} \
--include {input.include} \
--exclude {input.exclude} \
--min-date {params.min_date} \
--query {params.query:q} \
--output-log {log} \
--output-sequences {output.sequences}
"""
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