Copy join-metadata-and-clades.py from monkeypox

join-metadata-and-clades.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+import argparse
+import re
+import sys
+import pandas as pd
+
+NEXTCLADE_JOIN_COLUMN_NAME = 'seqName'
+VALUE_MISSING_DATA = '?'
+
+column_map = {
+    "clade": "clade",
+    "outbreak": "outbreak",
+    "lineage": "lineage",
+    "coverage": "coverage",
+    "totalMissing": "missing_data",
+    "totalSubstitutions": "divergence",
+    "totalNonACGTNs": "nonACGTN",
+    "qc.missingData.status": "QC_missing_data",
+    "qc.mixedSites.status": "QC_mixed_sites",
+    "qc.privateMutations.status": "QC_rare_mutations",
+    "qc.frameShifts.status": "QC_frame_shifts",
+    "qc.stopCodons.status": "QC_stop_codons",
+    "frameShifts": "frame_shifts",
+    "isReverseComplement": "is_reverse_complement",
+#    "deletions": "deletions",
+#    "insertions": "insertions"
+#    "substitutions": "substitutions",
+#    "aaSubstitutions": "aaSubstitutions"
+}
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Joins metadata file with Nextclade clade output",
+    )
+    parser.add_argument("--metadata")
+    parser.add_argument("--nextclade")
+    parser.add_argument("--id-field")
+    parser.add_argument("-o", default=sys.stdout)
+    return parser.parse_args()
+
+def main():
+    args = parse_args()
+
+    metadata = pd.read_csv(args.metadata, index_col=args.id_field,
+                           sep='\t', low_memory=False, na_filter = False)
+
+    # Read and rename clade column to be more descriptive
+    clades = pd.read_csv(args.nextclade, index_col=NEXTCLADE_JOIN_COLUMN_NAME,
+                         sep='\t', low_memory=False, na_filter = False) \
+            .rename(columns=column_map)
+
+    clades.index = clades.index.map(lambda x: re.sub(" \|.*", "", x))
+
+    # Select columns in column map
+    clades = clades[list(column_map.values())]
+
+    # Separate long from short columns
+    short_metadata = metadata.iloc[:,:-2].copy()
+    long_metadata = metadata.iloc[:,-2:].copy()
+
+    # Concatenate on columns
+    result = pd.merge(
+        short_metadata, clades,
+        left_index=True,
+        right_index=True,
+        how='left'
+    )
+
+    # Add long columns to back
+    result = pd.concat([result, long_metadata], axis=1)
+
+    result.to_csv(args.o, index_label=args.id_field, sep='\t')
+
+
+if __name__ == '__main__':
+    main()