Level 1 Assembly

notebooks/build_compiler_test.ipynb

@@ -0,0 +1,175 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "87bdb42e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sbol2\n",
+    "from buildcompiler.buildcompiler import BuildCompiler\n",
+    "from buildcompiler.abstract_translator import extract_toplevel_definition"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "e60a9c84",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "design_doc = sbol2.Document()\n",
+    "design_doc.read(\"../tests/test_files/moclo_parts_circuit.xml\")\n",
+    "design = extract_toplevel_definition(design_doc)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "90648527",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "auth = \"51102d98-f852-4386-9ae8-7c5814d679c1\"\n",
+    "collections = [\n",
+    "    \"https://synbiohub.org/user/Gon/impl_test/impl_test_collection/1\",\n",
+    "    \"https://synbiohub.org/user/Gon/Enzyme_Implementations/Enzyme_Implementations_collection/1\",\n",
+    "]\n",
+    "buildcompiler = BuildCompiler(collections, \"https://synbiohub.org\", auth, None)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7c12e504",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[<sbol2.implementation.Implementation object at 0x10d99bf20>, <sbol2.implementation.Implementation object at 0x10dadc230>]\n",
+      "[<sbol2.implementation.Implementation object at 0x10dadc140>]\n",
+      "matched pJ23100_AB_A_B with DVK_AE_A_E on fusion site A!\n",
+      "matched pB0034_BC_B_C with pJ23100_AB_A_B on fusion site B!\n",
+      "matched pE0030_CD_C_D with pB0034_BC_B_C on fusion site C!\n",
+      "matched final component pB0015_DE_D_E with pE0030_CD_C_D and DVK_AE_A_E on fusion sites (D, E)!\n",
+      "Success with backbone: DVK_AE_A_E and plasmids: ['pJ23100_AB_A_B', 'pB0034_BC_B_C', 'pE0030_CD_C_D', 'pB0015_DE_D_E']\n",
+      "[Plasmid:\n",
+      "  Name: composite_1_A_B_C_D_E\n",
+      "  Plasmid Definition: https://SBOL2Build.org/composite_1/1\n",
+      "  Strain Definitions: [None]\n",
+      "  Plasmid Implementations: ['https://SBOL2Build.org/composite_1_impl/1']\n",
+      "  Strain Implementations: [None]\n",
+      "  Fusion Sites: ['A', 'B', 'C', 'D', 'E']\n",
+      "  Antibiotic Resistance: Kanamycin\n",
+      "]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(buildcompiler.restriction_enzyme_implementations)\n",
+    "print(buildcompiler.ligase_implementations)\n",
+    "\n",
+    "composite_plasmids = buildcompiler.assembly_lvl1(design, None)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "79fd0cb5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Pull chassis from sbh\n",
+    "chassis_doc = sbol2.Document()\n",
+    "\n",
+    "buildcompiler.sbh.pull(\n",
+    "    \"https://synbiohub.org/user/Gon/Chassis/Ecoli_DH5a/1/52b575c09496ebb3e2ef9e4c272c9e733134a874/share\",\n",
+    "    chassis_doc,\n",
+    ")\n",
+    "\n",
+    "\n",
+    "chassis = chassis_doc.moduleDefinitions[0]\n",
+    "\n",
+    "dummy_activity = sbol2.Activity(\"chassis_domestication\")\n",
+    "dummy_activity.name = \"acquisistion of chassis strain\"\n",
+    "dummy_activity.types = \"http://sbols.org/v2#build\"\n",
+    "\n",
+    "chassis_implementation = sbol2.Implementation(f\"{chassis.name}_impl\")\n",
+    "chassis_implementation.built = chassis.identity\n",
+    "chassis_implementation.wasGeneratedBy = dummy_activity\n",
+    "\n",
+    "chassis_doc.add(chassis_implementation)\n",
+    "chassis_doc.add(dummy_activity)\n",
+    "\n",
+    "# chassis_doc.write(\"chassis_impl.xml\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8f4ea67c",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'composite_plasmids' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[6]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m bacterial_transformation(\u001b[43mcomposite_plasmids\u001b[49m, chassis_implementation, chassis, final_doc)\n",
+      "\u001b[31mNameError\u001b[39m: name 'composite_plasmids' is not defined"
+     ]
+    }
+   ],
+   "source": [
+    "# bacterial_transformation(composite_plasmids, chassis_implementation, chassis, final_doc)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5553bfc3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'Valid.'"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# final_doc.write(\"fullbuild.xml\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (buildplanner)",
+   "language": "python",
+   "name": "buildplanner"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}