Add host taxonomic categories #8
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| if record[args.hostlatin_field] == "Canis lupus familiaris": | ||
| return "Domestic Dog" | ||
| elif record[args.hostlatin_field] == "Homo sapiens": | ||
| return "Human" | ||
| elif record[args.hostlatin_field] == "Bos taurus": | ||
| return "Cattle" | ||
| elif record[args.hostlatin_field] in ["Didelphis albiventris", "Elephas maximus", "Dasypus novemcinctus"]: | ||
| return "Other Mammal" | ||
| elif record[args.hostfamily_field] == "Mephitidae": | ||
| return "Skunk" | ||
| elif record[args.hostfamily_field] == "Canidae" and record[args.hostgenus_field] == "Vulpes": | ||
| return "Fox (Vulpes sp.)" | ||
| elif record[args.hostfamily_field] == "Procyonidae" and record[args.hostgenus_field] == "Procyon": | ||
| return "Raccoon" | ||
| else: | ||
| host_group = record[args.hostgroup_field].lower() | ||
| return replacements.get(host_group, record[args.hostgroup_field]) |
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code style nitpick
This long if/elif/else can be a little hard to follow. Thoughts on pulling out these individual checks into other dicts like replacements?
(pseudo-code)
latin_replacements = { "Canis lupus familiaris": "Domestic Dog", ... }
family_replacements = { "Mephitidae": "Skunk", ... }
group_replacements = { "odd-toed ungulates": "Other Ungulate", ... }
latin_field = record[args.hostlatin_field]
family_field = record[args.hostfamily_field]
group_field = record[args.hostgroup_field]
if latin_field in latin_replacements:
return latin_replacements[latin_field]
elif family_field in family_replacements:
return family_replacements[family_field]
elif group_field in group_replacements:
return group_replacements[group_field]
else:
return group_fieldThere was a problem hiding this comment.
Done in 618bbd5. Current version still uses elif for situations in which both the family and genus need to match certain values. Happy to incorporate further suggestions to make this more clear.
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Ah, thanks for pointing out the situations that match both family and genus. I totally missed that the first time!
Happy to leave as-is and this did get my brain thinking that we might be able to generalize this by mocking the hierarchical geo-location rules 🤔
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(Not asking for changes in this PR, just throwing out the idea to see if it makes sense!)
The host rules can be formatted like <group>/<family>/<genus>/<species>\t<new_host_label>
Picking a couple examples from your script:
| host_hierarchy | new_host_label |
|---|---|
| odd-toed ungulates/*/*/* | Other Ungulate |
| */Mephitidae/*/* | Skunk |
| */Canidae/Vulpes/* | Fox (Vulpes sp.) |
| */Procyonidae/Procyon/* | Raccoon |
| */*/*/Canis lupus familiaris | Domestic Dog |
Then the generalized script would match starting from group down to species.
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Created an official propose for augur curate format-host in nextstrain/augur#1586
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* Extract the Host Taxonomic ID numbers from the metadata output by NCBI Datasets * Obtain detailed taxonomic info for each host taxon by inputting the Host Taxonomic ID numbers into the NCBI Datasets Taxonomy Package using the `datasets download taxonomy` function * Add the detailed taxonomic info to the metadata
Assign host taxa to taxonomic categories that are relevant for rabies using a custom script during the `curate` workflow
Color by the new host category, host latin name, and host common name
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| latin_replacements = { | ||
| "Canis lupus familiaris": "Domestic Dog", | ||
| "Homo sapiens": "Human", | ||
| "Bos taurus": "Cattle", | ||
| "Didelphis albiventris": "Other Mammal", | ||
| "Elephas maximus": "Other Mammal", | ||
| "Dasypus novemcinctus": "Other Mammal"} | ||
| family_replacements = {"Mephitidae": "Skunk"} | ||
| group_replacements = { | ||
| "odd-toed ungulates": "Other Ungulate", | ||
| "even-toed ungulates & whales": "Other Ungulate", | ||
| "carnivores": "Other Carnivore", | ||
| "bats": "Bat", | ||
| "birds": "Bird", | ||
| "primates": "Other Mammal", | ||
| "rodents": "Other Mammal", | ||
| "mammals": "Other Mammal" | ||
| } |
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non-blocking, but this would end up being more generic (and hence easier to ultimately move into augur or re-use in other repos) if these were provided via config files passed as CLI args.
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For sure! I wasn't sure how to make the config file generalized, but it just occurred to me that we can borrow the format of the hierarchical geolocation rules.
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Let's discuss the generic version in nextstrain/augur#1586
Description of proposed changes
Assigns host taxa to taxonomic groupings that are relevant to rabies for coloring in auspice through the following steps:
datasets download taxonomyfunctionNOTE: Testing this PR requires running the ingest workflow and then copy/pasting the output from
ingest/resultstophylogenetic/data. This is because the ingest output that is updated daily on S3 does not include the modifications that are made by the ingest workflow and used in the phylogenetic workflow in this PR.An example tree generated with these changes can be viewed here
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