bugfix, output copy number to shap output csv.

17_apply_to_proteome.py

@@ -289,6 +289,8 @@ if __name__ == '__main__':
             d6['accession'] = args.protein_fasta
             d6.to_csv(args.output_annotations, sep="\t", index=False)
             logging.info("Wrote annotation table to {}".format(args.output_annotations))
+            # d6 is a shallow copy, so reset columns
+            d5 = d5[header]
 
     if args.models is None:
         logging.info("Skipping model application, since no models were specified")
@@ -342,6 +344,7 @@ if __name__ == '__main__':
 
                 pl.DataFrame({
                     'rank': range(1, len(all_shaps) + 1),
+                    'copy_number': list(d5.iloc[:, all_shaps].values[0]),
                     'shap_value': list(shap_values[:, all_shaps].mean(0)),
                     'abs_shap_value': list(np.abs(shap_values[:, all_shaps]).mean(0)),
                     'gene': list(all_shaps_names),