Test mariana

examples/notebooks/test.ipynb

@@ -0,0 +1,49 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Hello\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(\"Hello\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "helical-package",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

helical/models/uce/model.py

@@ -98,6 +98,11 @@ def process_data(self,
         """
 
         self.check_rna_data_validity(data, gene_column_name)
+
+        list_of_mariana = [1,2,3]
+        if 1 in list_of_mariana:
+            # do my change
+
         if gene_column_name != "index":
             data.var.index = data.var[gene_column_name]
 
@@ -134,6 +139,7 @@ def process_data(self,
         pe_row_idxs = get_protein_embeddings_idxs(files_config["offset_pkl_path"], species, species_to_all_gene_symbols, filtered_adata)
         dataset_chroms, dataset_start = get_positions(Path(files_config["spec_chrom_csv_path"]), species, filtered_adata)
 
+
         if not (len(dataset_chroms) == len(dataset_start) == num_genes == pe_row_idxs.shape[0]): 
             LOGGER.error(f'Invalid input dimensions for the UCEDataset! ' 
                         f'dataset_chroms: {len(dataset_chroms)}, '