Refactor post-processing script to be specific to zika strain name fixes

This commit refactors the generic post-processing script to better align
with its specific purpose in Zika ingest. The purpose of this script is
to fix zika strain names based on historical modifications from the fauna
repo. In summary the following changes:

* Rename script to fix-zika-strain-names.py to match the purpose
* Add a docstring to the script
* Replace the accession argument with a strain field argument, which is
  the field that needs to be fixed

ingest/bin/post_process_metadata.py → ingest/bin/fix-zika-strain-names.py

@@ -8,10 +8,10 @@
 
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="Reformat a NCBI Virus metadata.tsv file for a pathogen build."
+        description="Modify zika strain names by referencing historical modifications from the fauna repo."
     )
-    parser.add_argument("--accession-field", default='accession',
-        help="Field from the records to use as the sequence ID in the FASTA file.")
+    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()
 
@@ -48,8 +48,7 @@ def main():
 
     for index, record in enumerate(stdin):
         record = json.loads(record)
-        record["strain"] = _set_strain_name(record)
-        record["authors"] = record["abbr_authors"]
+        record[args.strain_field] = _set_strain_name(record)
         stdout.write(json.dumps(record) + "\n")
 
 

ingest/rules/transform.smk

@@ -85,8 +85,7 @@ rule transform:
                 --abbr-authors-field {params.abbr_authors_field} \
             | ./vendored/apply-geolocation-rules \
                 --geolocation-rules {input.all_geolocation_rules} \
-            | ./bin/post_process_metadata.py \
-                --accession-field {params.id_field} \
+            | ./bin/fix-zika-strain-names.py \
             | ./vendored/merge-user-metadata \
                 --annotations {input.annotations} \
                 --id-field {params.annotations_id} \