replace post processing Rscript with python

ingest/bin/post_process_metadata.py

@@ -0,0 +1,91 @@
+#! /usr/bin/env python3
+
+"""Reformat pandas DataTables for a pathogen build.
+
+Expecting one argument, a NCBI Virus metadata.tsv file
+"""
+# ===== Dependencies
+import argparse
+import os
+import sys
+
+import numpy as np
+import pandas as pd
+
+
+def parse_args():
+  # Main help command
+  parser = argparse.ArgumentParser(
+    description = "USAGE: python post_process_metadata.py --metadata 'data/metadata.tsv'"
+  )
+  # Add first argument
+  parser.add_argument(
+    "--metadata",
+    help = "NCBI Virus metadata.tsv file.",
+    required = True
+  )
+  parser.add_argument(
+    "--outfile", default="processed_metadata.tsv",
+    help = "Processed metdata file name. [default: processed_metadata.tsv] ",
+    required = False
+  )
+
+  return parser.parse_args()
+
+# === Private methods
+
+def _set_strain_name(record):
+  """Check Isolate_s and Strain_s to find the strain name"""
+  strain_name=""
+  if record['strain'] != record['accession']:
+    strain_name=record['strain']
+  elif record['strain'] == record['accession'] and pd.notna(record['strain_s']):
+    strain_name=record['strain_s']
+  else:
+    strain_name=record['strain']
+
+  return strain_name.replace(' ', '_').replace('-',"_").replace(".","_").replace("(","_").replace(")","_")
+
+def _set_url(record):
+  """Set url column from accession"""
+  return "https://www.ncbi.nlm.nih.gov/nuccore/" + record['accession']
+
+def _set_paper_url(record):
+  """Set paper_url from publication"""
+  if pd.notna(record['publications']):
+    return "https://www.ncbi.nlm.nih.gov/pubmed/" + record['publications']
+  return ""
+
+def _set_dengue_serotype(record):
+  """Set dengue serotype from viruslineage_ids"""
+  if "11053" in record['viruslineage_ids']:
+    return "denv1"
+  elif "11060" in record['viruslineage_ids']:
+    return "denv2"
+  elif "11069" in record['viruslineage_ids']:
+    return "denv3"
+  elif "11070" in record['viruslineage_ids']:
+    return "denv4"
+  else:
+    return ""
+
+# === Main Method
+def main():
+  args = parse_args()
+  df=pd.read_csv(args.metadata, sep='\t', header=0)
+
+  # Mutate commands
+  df['strain'] = df.apply(_set_strain_name, axis=1)
+  df['url'] = df.apply(_set_url, axis=1)
+  df['paper_url'] = df.apply(_set_paper_url, axis=1)
+  df['serotype'] = df.apply(_set_dengue_serotype, axis=1)
+  df['authors'] = df['abbr_authors']
+  df['city'] = df['location']
+
+  # Format output
+  METADATA_COLUMNS = ["strain", "accession", "genbank_accession_rev","serotype", "date", "updated", "region", "country", "division", "city", "authors", "url", "title", "paper_url"]
+  df = df.reindex(METADATA_COLUMNS, axis=1)
+  df.to_csv(args.outfile, sep='\t', index=False)
+
+if __name__ == '__main__':
+  main()

ingest/workflow/snakemake_rules/transform.smk

@@ -128,7 +128,7 @@ rule post_process_metadata:
         metadata="data/metadata_{serotype}.tsv",
     shell:
        """
-       ./bin/post_process_metadata.R {input.metadata} {output.metadata}
+       ./bin/post_process_metadata.py --metadata {input.metadata} --outfile {output.metadata}
        """
 
 rule compress: