Merge pull request #8 from nextstrain/add-host-categories

Add host taxonomic categories

CHANGELOG.md

@@ -1,4 +1,5 @@
 # CHANGELOG
+* 20 August 2024: Assign host taxa to taxonomic groupings that are relevant to rabies for coloring in auspice
 * 12 August 2024: Create a full genome phylogeny for rabies [PR#3](https://github.com/nextstrain/rabies/pull/3)
 * 25 July 2024: Add CI GH Action workflow to test the ingest workflow [PR#6](https://github.com/nextstrain/rabies/pull/6)
 * 15 July 2024: Make rabies-specific modifications to the ingest directory (which originated from the pathogen-repo-guide) [PR#2](https://github.com/nextstrain/rabies/pull/2)

ingest/defaults/config.yaml

@@ -23,6 +23,7 @@ ncbi_datasets_fields:
   - update-date
   - length
   - host-name
+  - host-tax-id
   - isolate-lineage-source
   - biosample-acc
   - submitter-names
@@ -53,12 +54,18 @@ curate:
     release-date: date_released
     update-date: date_updated
     length: length
-    host-name: host
+    host-name: host_latin_name
+    host-tax-id: host_tax_id
     isolate-lineage-source: sample_type
     biosample-acc: biosample_accessions
     submitter-names: authors
     submitter-affiliation: institution
     submitter-country: submitter_country
+    Group name: host_group
+    Curator common name: host_common_name
+    Family name: host_family
+    Genus name: host_genus
+
   # Standardized strain name regex
   # Currently accepts any characters because we do not have a clear standard for strain names across pathogens
   strain_regex: "^.+$"
@@ -109,6 +116,11 @@ curate:
     "location",
     "length",
     "host",
+    "host_latin_name",
+    "host_family",
+    "host_genus",
+    "host_group",
+    "host_common_name",
     "date_released",
     "date_updated",
     "sra_accessions",

ingest/rules/curate.smk

@@ -107,6 +107,9 @@ rule curate:
                 --abbr-authors-field {params.abbr_authors_field} \
             | augur curate apply-geolocation-rules \
                 --geolocation-rules {input.all_geolocation_rules} \
+            | scripts/add-host-categories.py \
+            --latin-field host_latin_name --family-field host_family \
+            --genus-field host_genus --group-field host_group  \
             | augur curate apply-record-annotations \
                 --annotations {input.annotations} \
                 --id-field {params.annotations_id} \

ingest/rules/fetch_from_ncbi.smk

@@ -95,6 +95,67 @@ rule format_ncbi_dataset_report:
             > {output.ncbi_dataset_tsv}
         """
 
+rule extract_ncbi_dataset_hosttaxid:
+    input:
+        ncbi_dataset_tsv="data/ncbi_dataset_report.tsv",
+    output:
+        ncbi_dataset_hosttaxid="data/ncbi_dataset_hosttaxid.tsv",
+    log:
+        "logs/extract_ncbi_dataset_hosttaxid.txt",
+    benchmark:
+        "benchmarks/extract_ncbi_dataset_hosttaxid.txt"
+    shell:
+        """
+        tsv-select {input.ncbi_dataset_tsv} -H -f 'host\-tax\-id' | \
+        tsv-filter --is-numeric 1 | \
+        tsv-uniq \
+        2> {log} > {output.ncbi_dataset_hosttaxid}
+        """
+
+rule get_ncbi_hosttax_info:
+    input:
+        ncbi_dataset_hosttaxid="data/ncbi_dataset_hosttaxid.tsv",
+    output:
+        ncbi_hosttax_info="data/hosttax_info.zip",
+    # Allow retries in case of network errors
+    retries: 5
+    log:
+        "logs/get_ncbi_hosttax_info.txt",
+    benchmark:
+        "benchmarks/get_ncbi_hosttax_info.txt"
+    shell:
+        """
+        datasets download taxonomy taxon \
+        --inputfile {input.ncbi_dataset_hosttaxid} \
+        --filename {output.ncbi_hosttax_info} \
+        2>&1 | tee {log}
+        """
+
+rule join_metadata_and_hostinfo:
+    input:
+        ncbi_hosttax_info="data/hosttax_info.zip",
+        ncbi_dataset_tsv="data/ncbi_dataset_report.tsv",
+    output:
+        metadata = "data/metadata_with_taxinfo.tsv",
+    log:
+        "logs/join_metadata_and_hostinfo.txt",
+    benchmark:
+        "benchmarks/join_metadata_and_hostinfo.txt"
+    params:
+        ncbi_hosttax_columns = "Query,'Group\ name','Curator\ common\ name','Family\ name','Genus\ name'"
+    shell:
+        """
+        unzip -p {input.ncbi_hosttax_info} ncbi_dataset/data/taxonomy_summary.tsv \
+        | tsv-select -H -f {params.ncbi_hosttax_columns} \
+        | tsv-join -H \
+        --filter-file - \
+        --key-fields Query \
+        --data-fields 'host\-tax\-id' \
+        --append-fields '*' \
+        --write-all ? \
+        {input.ncbi_dataset_tsv} \
+        2> {log} > {output.metadata}
+        """
 
 # Technically you can bypass this step and directly provide FASTA and TSV files
 # as input files for the curate pipeline.
@@ -103,7 +164,7 @@ rule format_ncbi_dataset_report:
 rule format_ncbi_datasets_ndjson:
     input:
         ncbi_dataset_sequences="data/ncbi_dataset_sequences.fasta",
-        ncbi_dataset_tsv="data/ncbi_dataset_report.tsv",
+        ncbi_dataset_tsv="data/metadata_with_taxinfo.tsv",
     output:
         ndjson="data/ncbi.ndjson",
     log:

ingest/scripts/add-host-categories.py

@@ -0,0 +1,70 @@
+#! /usr/bin/env python3
+"""
+From stdin, generates host names using info from the NCBI taxonomy output of the NDJSON record, with output to 'host'
+
+Outputs the modified record to stdout.
+"""
+
+import argparse
+import json
+from sys import stdin, stdout
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Generate host names and output to 'host'.")
+    parser.add_argument("--latin-field", default='host_latin_name',
+        help="Field from the records to use as the host latin name.")
+    parser.add_argument("--family-field", default='host_family',
+        help="Field from the records to use as the host Family name.")
+    parser.add_argument("--genus-field", default='host_genus',
+        help="Field from the records to use as the host genus name.")
+    parser.add_argument("--group-field", default='host_group',
+        help="Field from the records to use as the host group.")
+    return parser.parse_args()
+
+def _set_host_name_transformed(record, args):
+    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"
+    }
+    latin_field = record[args.latin_field]
+    family_field = record[args.family_field]
+    group_field = record[args.group_field]
+
+    if record[args.family_field] == "Canidae" and record[args.genus_field] == "Vulpes":
+        return "Fox (Vulpes sp.)"
+    elif record[args.family_field] == "Procyonidae" and record[args.genus_field] == "Procyon":
+        return "Raccoon"
+    elif 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_field
+
+def main():
+    args = parse_args()
+
+    for index, record in enumerate(stdin):
+        record = json.loads(record)
+        record['host'] = _set_host_name_transformed(record, args)
+        stdout.write(json.dumps(record) + "\n")
+
+if __name__ == "__main__":
+    main()

phylogenetic/defaults/auspice_config.json

@@ -31,6 +31,16 @@
       "key": "host",
       "title": "Host",
       "type": "categorical"
+    },
+    {
+      "key": "host_latin_name",
+      "title": "Host latin name",
+      "type": "categorical"
+    },
+    {
+      "key": "host_common_name",
+      "title": "Host common name",
+      "type": "categorical"
     }
   ],
   "geo_resolutions": [
@@ -39,7 +49,7 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "region"
+    "color_by": "host"
   },
   "filters": [
     "region",

phylogenetic/defaults/colors.tsv

@@ -5,3 +5,16 @@ region	Africa	#8ABB6A
 region	Europe	#BEBB48
 region	South America	#E29E39
 region	North America	#E2562B
+#
+# Host taxa
+host	Bat	#3F47C9
+host	Domestic Dog	#4274CE
+host	Fox (Vulpes sp.)	#4F97BB
+host	Raccoon	#64AC99
+host	Skunk	#7EB976
+host	Other Carnivore	#9EBE5A
+host	Cattle	#BEBB48
+host	Other Ungulate	#D9AE3E
+host	Human	#E69036
+host	Other Mammal	#E35F2D
+host	Bird	#DB2823