example.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "\n",
    "from graphviz import Digraph\n",
    "import networkx as nx\n",
    "import networkx.algorithms as nxa\n",
    "import re\n",
    "\n",
    "from dwave.system.samplers import DWaveSampler\n",
    "from dwave.system.composites import EmbeddingComposite\n",
    "from dwave.system import LeapHybridSampler\n",
    "\n",
    "import DeBruijnDNA\n",
    "import AcyclicGraphDNA\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "API_KEY = \"D-WAVE_OCEAN_SDK_API_KEY\" #API_KEY, register on https://www.dwavesys.com/take-leap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def solve_dwave(Q, API_KEY):\n",
    "    \"\"\"\n",
    "    Q = np.array([[-1, 1, 0], [1, -1, -2], [0, -2, -1]])\n",
    "    solve_dwave(Q)\n",
    "    \"\"\"\n",
    "    q = {}\n",
    "    size = len(Q)\n",
    "    for i in range(size):\n",
    "        for j in range(size):\n",
    "            q[(i,j)] = Q[i][j]\n",
    "            \n",
    "    sampler = LeapHybridSampler(token=API_KEY)\n",
    "    response = sampler.sample_qubo(q, num_reads=30, anneal_time=20)\n",
    "\n",
    "    result = []\n",
    "    for sample, energy in response.data(['sample', 'energy']): \n",
    "        result.append(sample)\n",
    "        result.append(energy)\n",
    "\n",
    "    result.append(response.info) # view timings\n",
    "    \n",
    "    return result"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Hamiltonian path De Bruijn graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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     "execution_count": 3,
     "metadata": {},
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   ],
   "source": [
    "seq = 'CATACACCTAA'\n",
    "kmer_len, suffix_len = 3, 2\n",
    "adj, node_labels = DeBruijnDNA.make_debr(seq, kmer_len=kmer_len, suffix_len=suffix_len)\n",
    "\n",
    "g, nodes = DeBruijnDNA.draw_graph(adj, node_labels, [], kmer_len = kmer_len)\n",
    "g.engine = 'circo'\n",
    "Q = DeBruijnDNA.to_qubo(adj)\n",
    "\n",
    "g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "target_energy = -np.sqrt(len(Q))\n",
    "solution = solve_dwave(Q, API_KEY=API_KEY)\n",
    "spins, energy = [solution[0][i] for i in solution[0].keys()], solution[1]\n",
    "\n",
    "g, nodes = DeBruijnDNA.draw_graph(adj, node_labels, path_spins=spins, kmer_len=kmer_len)\n",
    "g.engine = 'circo'\n",
    "g"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Hamiltonian path in acyclic graph\n",
    "\n",
    "### use spec for input gfa file: http://gfa-spec.github.io/GFA-spec/GFA1.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "segments: 50, links: 248, containments: 0, lines: 299\n",
      "\n",
      "nodes quantity: 100\n",
      "links quantity:  496\n"
     ]
    }
   ],
   "source": [
    "filename = \"phi-x.600l.gfa\"\n",
    "segments, links, containments = AcyclicGraphDNA.load_file(filename)\n",
    "\n",
    "initial_graph, adjacency_matrix, nodes_indices, nodes_labels, links_edges = AcyclicGraphDNA.get_initial_graph(segments, links)\n",
    "strand_graph = AcyclicGraphDNA.get_strand_graph(initial_graph)\n",
    "\n",
    "print('links quantity: ', len(links_edges))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "strand_adjacency_matrix size: 50\n"
     ]
    },
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     "execution_count": 6,
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   ],
   "source": [
    "strand_graph_adjacency_matrix = nx.to_numpy_matrix(strand_graph)\n",
    "print('strand_adjacency_matrix size:', len(strand_graph_adjacency_matrix))\n",
    "\n",
    "edges = np.argwhere(strand_graph_adjacency_matrix==1).tolist()\n",
    "nodes = list(strand_graph.nodes)\n",
    "g = AcyclicGraphDNA.draw_graph(nodes, solve_edges=[], edges=edges)\n",
    "g.engine = 'neato'\n",
    "\n",
    "g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "strand_graph_undirected = AcyclicGraphDNA.complement_to_undirected_graph(strand_graph)\n",
    "adjacency_matrix = nx.to_numpy_matrix(strand_graph_undirected)\n",
    "part_map, _ , _ = AcyclicGraphDNA.part_graph(cluster_number=3, adjacency_matrix=adjacency_matrix)\n",
    "\n",
    "graphs = []\n",
    "node_labels = list(strand_graph_undirected.nodes)\n",
    "for part, nodes_indices in part_map.items():\n",
    "    labels = [node_labels[i] for i in nodes_indices]\n",
    "    graphs.append(strand_graph.subgraph(labels))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "solve_edges=[]\n",
    "for pg in graphs:\n",
    "    adjacency_matrix = nx.to_numpy_matrix(pg)\n",
    "    edges_indices = np.argwhere(adjacency_matrix==1).tolist()\n",
    "\n",
    "    Q = AcyclicGraphDNA.to_qubo(adjacency_matrix)\n",
    "    target_energy = -2.0*len(adjacency_matrix)+2\n",
    "    solution = solve_dwave(Q, API_KEY=API_KEY)\n",
    "    spins, energy = [solution[0][i] for i in solution[0].keys()], solution[1]\n",
    "\n",
    "    solve_edges_idices=[]\n",
    "    for i in range(len(spins)):\n",
    "        if spins[i]==1:\n",
    "            solve_edges_idices.append(edges_indices[i])\n",
    "\n",
    "    node_labels = list(pg.nodes)\n",
    "    solve_edges_part = [(node_labels[e[0]], node_labels[e[1]]) for e in solve_edges_idices]\n",
    "    solve_edges+=solve_edges_part"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
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     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "g = AcyclicGraphDNA.draw_solution(graphs, strand_graph, strand_graph_undirected, part_map, solve_edges, show_all_edges=False)\n",
    "g.engine = 'circo'\n",
    "g"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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