Add measles-specific fixes to strain names

ingest/bin/fix-measles-strain-names.py

@@ -0,0 +1,60 @@
+#! /usr/bin/env python3
+"""
+Parses GenBank's 'strain' field of the NDJSON record from stdin and applies measles-specific strain name corrections
+based on historical modifications from the fauna repo.
+
+Outputs the modified record to stdout.
+"""
+
+import argparse
+import json
+from sys import stdin, stdout
+
+import re
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Modify measles strain names by referencing historical modifications from the fauna repo."
+    )
+    parser.add_argument("--strain-field", default='strain',
+        help="Field from the records to use as the strain name to be fixed.")
+
+    return parser.parse_args()
+
+
+def _set_strain_name(record):
+    """Replace spaces, dashes, and periods with underscores in strain name."""
+    strain_name = record["strain"]
+
+    strain_name = strain_name.replace('MVs/', '').replace('MVi/', '').replace('Mvi/', '')
+    strain_name = re.sub(r'[_ ]?\[([A-Z][0-9])\]$', r'/\1', strain_name)
+    strain_name = re.sub(r'\(([A-Z][0-9])\)$', r'/\1', strain_name)
+    strain_name = re.sub(r'_([A-Z][0-9])_$', r'/\1', strain_name)
+    strain_name = re.sub(r'[ ;]', r'_', strain_name)
+    strain_name = re.sub(r'//', r'/', strain_name)
+
+    try:
+        strain_name = 'V' + str(int(strain_name))
+    except ValueError:
+        pass
+
+    return (
+        strain_name.replace(" ", "_")
+        .replace("-", "_")
+        .replace(".", "_")
+        .replace("(", "_")
+        .replace(")", "_")
+    )
+
+
+def main():
+    args = parse_args()
+
+    for index, record in enumerate(stdin):
+        record = json.loads(record)
+        record[args.strain_field] = _set_strain_name(record)
+        stdout.write(json.dumps(record) + "\n")
+
+
+if __name__ == "__main__":
+    main()

ingest/rules/curate.smk

@@ -105,6 +105,7 @@ rule curate:
                 --abbr-authors-field {params.abbr_authors_field} \
             | ./vendored/apply-geolocation-rules \
                 --geolocation-rules {input.all_geolocation_rules} \
+            | ./bin/fix-measles-strain-names.py \
             | ./vendored/merge-user-metadata \
                 --annotations {input.annotations} \
                 --id-field {params.annotations_id} \