Add convenience script to readme

README.md

@@ -44,8 +44,44 @@ See [tests](tests/test_aliasor.py) for more examples.
 
 ## Installation
 
+Choose any of the following:
+
 ```bash
 pip install pango_aliasor
+conda install -c bioconda pango_aliasor
+mamba install -c bioconda pango_aliasor
+```
+
+## Convenience script
+
+If you have a `metadata.tsv` with a `pango_lineage` column and you simply want to add a `pango_lineage_unaliased` column, you can use the convenience script below:
+
+```py
+import pandas as pd
+from pango_aliasor.aliasor import Aliasor
+import argparse
+
+
+def add_unaliased_column(tsv_file_path, pango_column='pango_lineage', unaliased_column='pango_lineage_unaliased'):
+    aliasor = Aliasor()
+    def uncompress_lineage(lineage):
+        if not lineage or pd.isna(lineage):
+            return "?"
+        return aliasor.uncompress(lineage)
+
+    df = pd.read_csv(tsv_file_path, sep='\t')
+    df[unaliased_column] = df[pango_column].apply(uncompress_lineage)
+    return df
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Add unaliased Pango lineage column to a TSV file.')
+    parser.add_argument('--input-tsv', required=True, help='Path to the input TSV file.')
+    parser.add_argument('--pango-column', default='pango_lineage', help='Name of the Pango lineage column in the input file.')
+    parser.add_argument('--unaliased-column', default='pango_lineage_unaliased', help='Name of the column to use for the unaliased Pango lineage column in output.')
+    args = parser.parse_args()
+    df = add_unaliased_column(args.input_tsv, args.pango_column, args.unaliased_column)
+    print(df.to_csv(sep='\t', index=False))
 ```
 
 ## Testing