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Update Andersen Lab ingest to new metadata #64

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merged 4 commits into from
Jun 25, 2024
Merged

Update Andersen Lab ingest to new metadata #64

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92c6b71
ingest/andersen-lab: Switch to new automated metadata
joverlee521 Jun 25, 2024
906a881
ingest/host-map: Add new hosts from Andersen Lab ingest
joverlee521 Jun 25, 2024
a27e9e4
Include admin division annotation for house mouse genomes
trvrb Jun 25, 2024
1297ecd
ingest/host-map: Support comments and correct `HOSP`
joverlee521 Jun 25, 2024
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8 changes: 6 additions & 2 deletions ingest/build-configs/ncbi/bin/transform-host
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,13 @@ def parse_host_map(host_map_file: str) -> dict:
"""
host_map = {}
with open(host_map_file) as tsv_file:
reader = csv.DictReader(tsv_file, delimiter="\t")
reader = csv.reader(tsv_file, delimiter="\t")
for row in reader:
host_map[row["old_name"].lower()] = row["new_name"]
# Skip comments
if not row or row[0].lstrip()[0] == '#':
continue

host_map[row[0].lower()] = row[1]

return host_map

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2 changes: 2 additions & 0 deletions ingest/build-configs/ncbi/defaults/annotations.tsv
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Expand Up @@ -8,3 +8,5 @@ A/environment/USA/CO-UW-9084466/2024 division Colorado # Based on linked BioSamp
A/environment/USA/CO-UW-9084466/2024 host Cattle # This sequence from commercial milk is definitively from cattle, strain name guidelines are going to be updated here
A/ALPACA/USA/24-014328-007/2024 division Idaho # Based on news reports https://www.cidrap.umn.edu/avian-influenza-bird-flu/alpacas-infected-h5n1-avian-flu-idaho
A/Alpaca/USA/24-015080-001/2024 division Idaho # Based on news reports https://www.cidrap.umn.edu/avian-influenza-bird-flu/alpacas-infected-h5n1-avian-flu-idaho
A/House-Mouse/USA/24-014780-002/2024 division New Mexico # Based on https://wahis.woah.org/#/in-review/4451?reportId=167771&fromPage=event-dashboard-url
A/House-Mouse/USA/24-014782-003/2024 division New Mexico # Based on https://wahis.woah.org/#/in-review/4451?reportId=167771&fromPage=event-dashboard-url
4 changes: 3 additions & 1 deletion ingest/build-configs/ncbi/defaults/host-map.tsv
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@@ -1,4 +1,4 @@
old_name new_name
# Check for bird codes in https://www.carolinabirdclub.org/bandcodes.html
alpaca Nonhuman Mammal
american crow Avian
american wigeon Avian
Expand Down Expand Up @@ -50,6 +50,8 @@ harris hawk Avian
harris-hawk Avian
hawk Avian
Homo sapiens Human
HOSP Avian
House-Mouse Nonhuman Mammal
Icteridae Avian
Larus occidentalis Avian
Lophodytes cucullatus Avian
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10 changes: 5 additions & 5 deletions ingest/build-configs/ncbi/rules/ingest_andersen_lab.smk
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Expand Up @@ -39,9 +39,9 @@ rule extract_automated_metadata:
input:
andersen_lab_repo = "andersen-lab/data/avian-influenza.tar.gz"
output:
metadata = "andersen-lab/data/PRJNA1102327_automated_metadata.csv"
metadata = "andersen-lab/data/SraRunTable_automated_metadata.csv",
params:
metadata_file_path = "metadata/SraRunTable_PRJNA1102327_automated.csv",
metadata_file_path = "metadata/SraRunTable_automated.csv",
shell:
"""
tar xz -O --file={input.andersen_lab_repo} \
Expand All @@ -58,9 +58,9 @@ rule join_old_and_automated_metadata:
"""
input:
old_metadata = "andersen-lab/data/PRJNA1102327_old_metadata.csv",
automated_metadata = "andersen-lab/data/PRJNA1102327_automated_metadata.csv",
automated_metadata = "andersen-lab/data/SraRunTable_automated_metadata.csv",
output:
metadata = "andersen-lab/data/PRJNA1102327_metadata.csv",
metadata = "andersen-lab/data/raw_metadata.csv",
params:
join_field = "Run",
shell:
Expand Down Expand Up @@ -114,7 +114,7 @@ rule rename_and_concatenate_segment_fastas:

rule curate_metadata:
input:
metadata = "andersen-lab/data/PRJNA1102327_metadata.csv",
metadata = "andersen-lab/data/raw_metadata.csv",
geolocation_rules = "defaults/geolocation_rules.tsv",
annotations=config["curate"]["annotations"],
output:
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