nucleotide-transformer.2.inference.ipynb

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      "######### test ravel ############\n",
      "sequences:\n",
      "[['A' 'B']\n",
      " ['C' 'D']\n",
      " ['E' 'F']\n",
      " ['G' 'H']]\n",
      "(4, 2)\n",
      "raveled sequences:\n",
      "['A' 'B' 'C' 'D' 'E' 'F' 'G' 'H']\n",
      "(8,)\n",
      "######### test unravel ############\n",
      "embeddings:\n",
      "[[ 1  2  3]\n",
      " [ 4  5  6]\n",
      " [ 7  8  9]\n",
      " [10 11 12]\n",
      " [13 14 15]\n",
      " [16 17 18]\n",
      " [19 20 21]\n",
      " [22 23 24]]\n",
      "(8, 3)\n",
      "unraveled embeddings:\n",
      "[[[ 1  2  3]\n",
      "  [ 4  5  6]]\n",
      "\n",
      " [[ 7  8  9]\n",
      "  [10 11 12]]\n",
      "\n",
      " [[13 14 15]\n",
      "  [16 17 18]]\n",
      "\n",
      " [[19 20 21]\n",
      "  [22 23 24]]]\n",
      "(4, 2, 3)\n"
     ]
    }
   ],
   "source": [
    "CONSTRAINT_TOOLS = '/scratch/ucgd/lustre-work/quinlan/u6018199/constraint-tools'\n",
    "CONSTRAINT_TOOLS_DATA = '/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools'\n",
    "\n",
    "import numpy as np \n",
    "\n",
    "import sys\n",
    "sys.path.append(f'{CONSTRAINT_TOOLS}/utilities')\n",
    "\n",
    "from ravel_unravel import ravel, unravel\n",
    "\n",
    "def test_ravel():\n",
    "  print('######### test ravel ############')\n",
    "  sequences = np.array([['A','B'], ['C','D'], ['E','F'], ['G','H']]) # 4 alleles, 2 sites\n",
    "  print('sequences:')\n",
    "  print(sequences)\n",
    "  print(sequences.shape)\n",
    "\n",
    "  sequences_raveled = ravel(sequences)\n",
    "  print('raveled sequences:')\n",
    "  print(sequences_raveled)\n",
    "  print(sequences_raveled.shape)\n",
    "\n",
    "  comparison = sequences_raveled == ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']\n",
    "  assert comparison.all()\n",
    "\n",
    "test_ravel() \n",
    "\n",
    "def test_unravel(): \n",
    "  print('######### test unravel ############')\n",
    "  embeddings = [\n",
    "    [1,2,3],\n",
    "    [4,5,6],\n",
    "    [7,8,9],\n",
    "    [10,11,12],\n",
    "    [13,14,15],\n",
    "    [16,17,18],\n",
    "    [19,20,21],\n",
    "    [22,23,24]\n",
    "  ]\n",
    "  embeddings = np.array(embeddings) \n",
    "  print('embeddings:')\n",
    "  print(embeddings)\n",
    "  print(embeddings.shape)\n",
    "\n",
    "  embeddings_unraveled = unravel(embeddings, number_alleles=4, number_sites=2)\n",
    "  print('unraveled embeddings:')\n",
    "  print(embeddings_unraveled)\n",
    "  print(embeddings_unraveled.shape)\n",
    "\n",
    "  comparison = embeddings_unraveled == np.array([\n",
    "    [[ 1,  2,  3], [ 4,  5,  6]],\n",
    "    [[ 7,  8,  9], [10, 11, 12]],\n",
    "    [[13, 14, 15], [16, 17, 18]],\n",
    "    [[19, 20, 21], [22, 23, 24]]\n",
    "  ])\n",
    "  assert comparison.all()\n",
    "\n",
    "test_unravel()\n"
   ]
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