Parameterize ncbi_id in fetch_sequences

ingest/bin/fetch-from-genbank

@@ -7,12 +7,14 @@ set -euo pipefail
 
 bin="$(dirname "$0")"
 
+
 main() {
-    fetch | "$bin"/csv-to-ndjson
+    local ncbi_taxon_id="${1:?NCBI taxon id is required.}"
+    fetch "$ncbi_taxon_id" | "$bin"/csv-to-ndjson
 }
 
 fetch() {
-    curl "$("$bin"/genbank-url)" \
+    curl "$("$bin"/genbank-url --ncbi-taxon-id "$1")" \
         --fail --silent --show-error --http1.1 \
         --header 'User-Agent: https://github.com/nextstrain/monkeypox (hello@nextstrain.org)'
 }

ingest/bin/genbank-url

@@ -12,54 +12,80 @@ and observing the network activity at
     https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Monkeypox%20virus,%20taxid:10244
 """
 from urllib.parse import urlencode
+import argparse
 
-endpoint = "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/"
-params = {
-    # Search criteria
-    'fq': [
-        '{!tag=SeqType_s}SeqType_s:("Nucleotide")', # Nucleotide sequences (as opposed to protein)
-        'VirusLineageId_ss:(10244)',                # NCBI Taxon id for Monkeypox
-    ],
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Given an NCBI taxon ID, generate URL to download "
+        "all viral sequences and their curated metadata from GenBank via NCBI Virus."
+    )
+    parser.add_argument(
+        "--ncbi-taxon-id",
+        help="NCBI Taxon ID.",
+        default="10244",
+        required=True
+    )
+    return parser.parse_args()
 
-    # Unclear, but seems necessary.
-    'q': '*:*',
+def build_query_url(ncbi_taxon_id: str):
+    """
+    Generate URL to download all viral sequences and their curated metadata
+    from GenBank via NCBI Virus.
+    """
+    endpoint = "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/"
+    params = {
+        # Search criteria
+        'fq': [
+            '{!tag=SeqType_s}SeqType_s:("Nucleotide")', # Nucleotide sequences (as opposed to protein)
+            f'VirusLineageId_ss:({ncbi_taxon_id})',                # NCBI Taxon id for Monkeypox
+        ],
 
-    # Response format
-    'cmd': 'download',
-    'dlfmt': 'csv',
-    'fl': ','.join(
-        ':'.join(names) for names in [
-            # Pairs of (output column name, source data field).
-            ('genbank_accession',       'id'),
-            ('genbank_accession_rev',   'AccVer_s'),
-            ('database',                'SourceDB_s'),
-            ('strain',                  'Isolate_s'),
-            ('region',                  'Region_s'),
-            ('location',                'CountryFull_s'),
-            ('collected',               'CollectionDate_s'),
-            ('submitted',               'CreateDate_dt'),
-            ('length',                  'SLen_i'),
-            ('host',                    'Host_s'),
-            ('isolation_source',        'Isolation_csv'),
-            ('bioproject_accession',    'BioProject_s'),
-            ('biosample_accession',     'BioSample_s'),
-            ('sra_accession',           'SRALink_csv'),
-            ('title',                   'Definition_s'),
-            ('authors',                 'Authors_csv'),
-            ('submitting_organization', 'SubmitterAffilFull_s'),
-            ('publications',            'PubMed_csv'),
-            ('sequence',                'Nucleotide_seq'),
-        ]
-    ),
+        # Unclear, but seems necessary.
+        'q': '*:*',
 
-    # Stable sort with GenBank accessions.
-    # Columns are source data fields, not our output columns.
-    'sort': 'id asc',
+        # Response format
+        'cmd': 'download',
+        'dlfmt': 'csv',
+        'fl': ','.join(
+            ':'.join(names) for names in [
+                # Pairs of (output column name, source data field).
+                ('genbank_accession',       'id'),
+                ('genbank_accession_rev',   'AccVer_s'),
+                ('database',                'SourceDB_s'),
+                ('strain',                  'Isolate_s'),
+                ('region',                  'Region_s'),
+                ('location',                'CountryFull_s'),
+                ('collected',               'CollectionDate_s'),
+                ('submitted',               'CreateDate_dt'),
+                ('length',                  'SLen_i'),
+                ('host',                    'Host_s'),
+                ('isolation_source',        'Isolation_csv'),
+                ('bioproject_accession',    'BioProject_s'),
+                ('biosample_accession',     'BioSample_s'),
+                ('sra_accession',           'SRALink_csv'),
+                ('title',                   'Definition_s'),
+                ('authors',                 'Authors_csv'),
+                ('submitting_organization', 'SubmitterAffilFull_s'),
+                ('publications',            'PubMed_csv'),
+                ('sequence',                'Nucleotide_seq'),
+            ]
+        ),
 
-    # This isn't Entrez, but include the same email parameter it requires just
-    # to be nice.
-    'email': 'hello@nextstrain.org',
-}
-query = urlencode(params, doseq = True, encoding = "utf-8")
+        # Stable sort with GenBank accessions.
+        # Columns are source data fields, not our output columns.
+        'sort': 'id asc',
 
-print(f"{endpoint}?{query}")
+        # This isn't Entrez, but include the same email parameter it requires just
+        # to be nice.
+        'email': 'hello@nextstrain.org',
+    }
+    query = urlencode(params, doseq = True, encoding = "utf-8")
+
+    print(f"{endpoint}?{query}")
+
+def main():
+    args = parse_args()
+    build_query_url(args.ncbi_taxon_id)
+
+if __name__ == '__main__':
+    main()

ingest/workflow/snakemake_rules/fetch_sequences.smk

@@ -19,7 +19,7 @@ rule fetch_from_genbank:
         genbank_ndjson="data/genbank.ndjson",
     shell:
         """
-        ./bin/fetch-from-genbank > {output.genbank_ndjson}
+        ./bin/fetch-from-genbank 10244 > {output.genbank_ndjson}
         """