common.ipynb

{
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   "cell_type": "code",
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   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name '__file__' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-2eb8c59b22cb>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     16\u001b[0m \u001b[0;31m#set the data directory\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 17\u001b[0;31m \u001b[0mdir_path\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdirname\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrealpath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m__file__\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     18\u001b[0m \u001b[0mDATA_DIR\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdir_path\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\"../data\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     19\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDATA_DIR\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name '__file__' is not defined"
     ]
    }
   ],
   "source": [
    "#import basics\n",
    "import os\n",
    "import sys\n",
    "import re\n",
    "\n",
    "#import Python bioinformatics packages\n",
    "import Bio\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import pandas\n",
    "import h5py\n",
    "\n",
    "#import Hi-C packages and other lab-made tools\n",
    "import cooler\n",
    "\n",
    "#set the data directory\n",
    "dir_path = os.path.dirname(os.path.realpath(__file__))\n",
    "DATA_DIR = os.path.join(dir_path,\"../data\")\n",
    "print(DATA_DIR)"
   ]
  }
 ],
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