update notebooks

Author: manulera

docs/notebooks/Example_CRISPR.ipynb

@@ -219,17 +219,8 @@
    "outputs": [
     {
      "data": {
-      "text/html": [
-       "<pre>name|45\n",
-       "     \\/\n",
-       "     /\\\n",
-       "     45|My repair oligo for this experiment|45\n",
-       "                                            \\/\n",
-       "                                            /\\\n",
-       "                                            45|name</pre>"
-      ],
       "text/plain": [
-       "Contig(-469)"
+       "Dseqrecord(-469)"
       ]
      },
      "execution_count": null,
@@ -238,11 +229,10 @@
     }
    ],
    "source": [
-    "from pydna.assembly import Assembly\n",
+    "from pydna.assembly2 import in_vivo_assembly\n",
     "\n",
-    "my_KO = Assembly((target_dseq.cut(enzyme)[0],repair_oligo, target_dseq.cut(enzyme2)[-1]), limit = 20 )\n",
-    "my_assembly_KO, *rest = my_KO.assemble_linear()\n",
-    "my_assembly_KO"
+    "products = in_vivo_assembly((target_dseq.cut(enzyme)[0],repair_oligo, target_dseq.cut(enzyme2)[-1]), limit = 20 )\n",
+    "products[0]"
    ]
   }
  ],
@@ -262,7 +252,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,