fix bug

theislab · Dec 2, 2020 · 0dbe8df · 0dbe8df
1 parent 8168bcb
commit 0dbe8df
Showing 1 changed file with 13 additions and 71 deletions.
diff --git a/latest_notebook/Case-study_Mouse-intestinal-epithelium_1906.ipynb b/latest_notebook/Case-study_Mouse-intestinal-epithelium_1906.ipynb
@@ -110,10 +110,10 @@
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
      "output_type": "stream",
+     "name": "stdout",
      "text": [
-      "scanpy==1.4.3+80.g740c557 anndata==0.6.22rc1 umap==0.3.9 numpy==1.16.2 scipy==1.3.0 pandas==0.24.1 scikit-learn==0.20.2 statsmodels==0.10.0rc2 python-igraph==0.7.1 louvain==0.6.1\n"
+      "scanpy==1.4.6 anndata==0.7.1 umap==0.4.0 numpy==1.18.2 scipy==1.4.1 pandas==1.0.3 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.0 louvain==0.6.1\n"
      ]
     }
    ],
@@ -204,8 +204,8 @@
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
      "output_type": "stream",
+     "name": "stdout",
      "text": [
       "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836573_Regional_Duo_M1_matrix.h5ad\n"
      ]
@@ -247,75 +247,16 @@
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836574_Regional_Duo_M2_matrix.h5ad\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Making variable names unique for controlled concatenation.\n",
-      "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836575_Regional_Jej_M1_matrix.h5ad\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836576_Regional_Jej_M2_matrix.h5ad\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836577_Regional_Il_M1_matrix.h5ad\n"
-     ]
-    },
-    {
-     "name": "stderr",
      "output_type": "stream",
-     "text": [
-      "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n"
-     ]
-    },
-    {
      "name": "stdout",
-     "output_type": "stream",
      "text": [
+      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836574_Regional_Duo_M2_matrix.h5ad\n",
+      "Making variable names unique for controlled concatenation.\n",
+      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836575_Regional_Jej_M1_matrix.h5ad\n",
+      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836576_Regional_Jej_M2_matrix.h5ad\n",
+      "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836577_Regional_Il_M1_matrix.h5ad\n",
       "... reading from cache file cache/..-data-Haber-et-al_mouse-intestinal-epithelium-GSE92332_RAW-GSM2836578_Regional_Il_M2_matrix.h5ad\n"
      ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n"
-     ]
     }
    ],
    "source": [
@@ -351,8 +292,9 @@
     "\n",
     "    # Concatenate to main adata object\n",
     "    adata = adata.concatenate(adata_tmp, batch_key='sample_id')\n",
-    "    adata.var['gene_id'] = adata.var['gene_id-1']\n",
-    "    adata.var.drop(columns = ['gene_id-1', 'gene_id-0'], inplace=True)\n",
+    "    if 'gene_id_1' in adata.var.columns:\n",
+    "        adata.var['gene_id'] = adata.var['gene_id-1']\n",
+    "        adata.var.drop(columns = ['gene_id-1', 'gene_id-0'], inplace=True)\n",
     "    adata.obs.drop(columns=['sample_id'], inplace=True)\n",
     "    adata.obs_names = [c.split(\"-\")[0] for c in adata.obs_names]\n",
     "    adata.obs_names_make_unique(join='_')"
@@ -6532,7 +6474,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.7-final"
   },
   "toc": {
    "base_numbering": "0",
@@ -6584,4 +6526,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}