{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "be5d3b4f",
   "metadata": {},
   "source": [
    "# Datasets\n",
    "\n",
    "Datasets consist of complete combinatorial landscapes to visualize and work with, as well as the data from which the were inferred. Both inference of the complete landscape and calculation of the coordinates of the visualization are precomputed to provide rapid access to the different layers of interest."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6b281ef0",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import required libraries\n",
    "import numpy as np\n",
    "\n",
    "from gpmap.datasets import DataSet, list_available_datasets\n",
    "from gpmap.inference import VCregression"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c419153e",
   "metadata": {},
   "source": [
    "## How to load a built-in dataset\n",
    "\n",
    "We include a series of datasets that are used throughout the documentation for demonstration of the different applications and are directly accessible after installation of the library for any user.\n",
    "The list of built-in datasets can be easily shown as follows"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "a40a04a0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['5ss', 'f1u', 'test', 'dmsc', 'gb1', 'smn1', 'serine', 'trna', 'pard']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list_available_datasets()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "508e43b7",
   "metadata": {},
   "source": [
    "### How to access combinatorial landscape values\n",
    "\n",
    "And one can easily load one of those datasets as illustrated in some previous tutorials, and all of them should contain at least a `landscape` attribute containing the phenotype associated to each possible genotype"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "b5b44e02",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>y</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>seq</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAAA</th>\n",
       "      <td>0.296301</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAC</th>\n",
       "      <td>-2.713474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAD</th>\n",
       "      <td>-2.912992</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAE</th>\n",
       "      <td>-4.548719</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAF</th>\n",
       "      <td>-3.276738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>YYYS</th>\n",
       "      <td>-4.662925</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYT</th>\n",
       "      <td>-3.223102</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYV</th>\n",
       "      <td>-3.001718</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYW</th>\n",
       "      <td>-4.723318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYY</th>\n",
       "      <td>-4.876429</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>160000 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             y\n",
       "seq           \n",
       "AAAA  0.296301\n",
       "AAAC -2.713474\n",
       "AAAD -2.912992\n",
       "AAAE -4.548719\n",
       "AAAF -3.276738\n",
       "...        ...\n",
       "YYYS -4.662925\n",
       "YYYT -3.223102\n",
       "YYYV -3.001718\n",
       "YYYW -4.723318\n",
       "YYYY -4.876429\n",
       "\n",
       "[160000 rows x 1 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gb1 = DataSet('gb1')\n",
    "gb1.landscape"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2ed7ddd0",
   "metadata": {},
   "source": [
    "### How to access the processed data in experimental datasets\n",
    "\n",
    "If the landscape was obtained from experimental data, then it also has a `data` attribute that includes the measurement `y` and, if available, its uncertainty `y_var`. \n",
    "The data may not necessarily include measurements for every possible sequence, as in this case, in which about ~10000 sequences were not experimentally measured"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "5ef03158",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>y</th>\n",
       "      <th>y_var</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sequence</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAAA</th>\n",
       "      <td>0.460831</td>\n",
       "      <td>0.046009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAG</th>\n",
       "      <td>-2.192261</td>\n",
       "      <td>0.255906</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAH</th>\n",
       "      <td>-4.728306</td>\n",
       "      <td>2.064530</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAI</th>\n",
       "      <td>-4.338842</td>\n",
       "      <td>2.095252</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAL</th>\n",
       "      <td>-2.326240</td>\n",
       "      <td>0.087518</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYS</th>\n",
       "      <td>-5.269987</td>\n",
       "      <td>0.291090</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYT</th>\n",
       "      <td>-3.821426</td>\n",
       "      <td>0.074489</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYV</th>\n",
       "      <td>-3.143536</td>\n",
       "      <td>0.074682</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYW</th>\n",
       "      <td>-4.306581</td>\n",
       "      <td>0.699467</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYY</th>\n",
       "      <td>-4.429813</td>\n",
       "      <td>0.417405</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>149361 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 y     y_var\n",
       "sequence                    \n",
       "AAAA      0.460831  0.046009\n",
       "AAAG     -2.192261  0.255906\n",
       "AAAH     -4.728306  2.064530\n",
       "AAAI     -4.338842  2.095252\n",
       "AAAL     -2.326240  0.087518\n",
       "...            ...       ...\n",
       "YYYS     -5.269987  0.291090\n",
       "YYYT     -3.821426  0.074489\n",
       "YYYV     -3.143536  0.074682\n",
       "YYYW     -4.306581  0.699467\n",
       "YYYY     -4.429813  0.417405\n",
       "\n",
       "[149361 rows x 2 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gb1.data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "47fdfd9a",
   "metadata": {},
   "source": [
    "### How to access the a dataset visualization\n",
    "\n",
    "For built-in datasets, we also provide the pre-calculated coordinates of the visualization, the `DataFrame` connecting sequences separated by single point mutations and the relaxation times associated to each of the diffusion axes in the attributes `nodes`, `edges` and `relaxation_times`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "f2bfbe60",
   "metadata": {},
   "outputs": [
    {
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       "      <th>5</th>\n",
       "      <th>6</th>\n",
       "      <th>7</th>\n",
       "      <th>8</th>\n",
       "      <th>9</th>\n",
       "      <th>10</th>\n",
       "      <th>function</th>\n",
       "      <th>stationary_freq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAAA</th>\n",
       "      <td>-0.270938</td>\n",
       "      <td>-0.944304</td>\n",
       "      <td>-0.227171</td>\n",
       "      <td>0.744803</td>\n",
       "      <td>0.059077</td>\n",
       "      <td>-0.077512</td>\n",
       "      <td>-0.477853</td>\n",
       "      <td>0.174491</td>\n",
       "      <td>0.015944</td>\n",
       "      <td>0.052664</td>\n",
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       "      <td>1.067767e-04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAC</th>\n",
       "      <td>0.033789</td>\n",
       "      <td>-0.232603</td>\n",
       "      <td>-0.271458</td>\n",
       "      <td>0.576487</td>\n",
       "      <td>0.035619</td>\n",
       "      <td>0.087608</td>\n",
       "      <td>0.590118</td>\n",
       "      <td>-0.249005</td>\n",
       "      <td>-0.087750</td>\n",
       "      <td>-0.110291</td>\n",
       "      <td>-2.713474</td>\n",
       "      <td>4.954648e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAD</th>\n",
       "      <td>-0.020398</td>\n",
       "      <td>-0.127749</td>\n",
       "      <td>-0.174455</td>\n",
       "      <td>0.347843</td>\n",
       "      <td>0.142684</td>\n",
       "      <td>0.208679</td>\n",
       "      <td>0.590025</td>\n",
       "      <td>0.160819</td>\n",
       "      <td>0.354397</td>\n",
       "      <td>0.676487</td>\n",
       "      <td>-2.912992</td>\n",
       "      <td>4.042194e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAE</th>\n",
       "      <td>-0.001018</td>\n",
       "      <td>-0.138712</td>\n",
       "      <td>-0.183161</td>\n",
       "      <td>0.340728</td>\n",
       "      <td>0.121067</td>\n",
       "      <td>0.157871</td>\n",
       "      <td>0.436407</td>\n",
       "      <td>0.195630</td>\n",
       "      <td>0.211100</td>\n",
       "      <td>0.364298</td>\n",
       "      <td>-4.548719</td>\n",
       "      <td>7.619345e-07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAF</th>\n",
       "      <td>0.149717</td>\n",
       "      <td>-0.156524</td>\n",
       "      <td>-0.239304</td>\n",
       "      <td>0.386243</td>\n",
       "      <td>0.103285</td>\n",
       "      <td>0.107756</td>\n",
       "      <td>0.302406</td>\n",
       "      <td>0.051575</td>\n",
       "      <td>0.171278</td>\n",
       "      <td>0.226772</td>\n",
       "      <td>-3.276738</td>\n",
       "      <td>2.789084e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYS</th>\n",
       "      <td>0.073880</td>\n",
       "      <td>0.038075</td>\n",
       "      <td>-0.097751</td>\n",
       "      <td>0.156184</td>\n",
       "      <td>0.056463</td>\n",
       "      <td>0.074291</td>\n",
       "      <td>0.262512</td>\n",
       "      <td>0.019037</td>\n",
       "      <td>0.144439</td>\n",
       "      <td>0.172686</td>\n",
       "      <td>-4.662925</td>\n",
       "      <td>6.781399e-07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYT</th>\n",
       "      <td>-0.091125</td>\n",
       "      <td>0.213370</td>\n",
       "      <td>0.256403</td>\n",
       "      <td>0.246274</td>\n",
       "      <td>-0.086279</td>\n",
       "      <td>0.026923</td>\n",
       "      <td>0.217086</td>\n",
       "      <td>0.102111</td>\n",
       "      <td>0.593257</td>\n",
       "      <td>0.003682</td>\n",
       "      <td>-3.223102</td>\n",
       "      <td>2.945947e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYV</th>\n",
       "      <td>0.016488</td>\n",
       "      <td>0.195242</td>\n",
       "      <td>0.216320</td>\n",
       "      <td>0.035269</td>\n",
       "      <td>0.306726</td>\n",
       "      <td>0.025334</td>\n",
       "      <td>0.217759</td>\n",
       "      <td>-0.028542</td>\n",
       "      <td>-0.038378</td>\n",
       "      <td>0.148356</td>\n",
       "      <td>-3.001718</td>\n",
       "      <td>3.692393e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYW</th>\n",
       "      <td>0.134072</td>\n",
       "      <td>0.114107</td>\n",
       "      <td>-0.043856</td>\n",
       "      <td>0.011092</td>\n",
       "      <td>0.076565</td>\n",
       "      <td>0.109907</td>\n",
       "      <td>0.261274</td>\n",
       "      <td>0.108909</td>\n",
       "      <td>0.180371</td>\n",
       "      <td>0.365348</td>\n",
       "      <td>-4.723318</td>\n",
       "      <td>6.376209e-07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YYYY</th>\n",
       "      <td>0.086278</td>\n",
       "      <td>0.113188</td>\n",
       "      <td>-0.035062</td>\n",
       "      <td>0.017597</td>\n",
       "      <td>0.096670</td>\n",
       "      <td>0.249598</td>\n",
       "      <td>0.261107</td>\n",
       "      <td>0.108695</td>\n",
       "      <td>0.188331</td>\n",
       "      <td>0.368750</td>\n",
       "      <td>-4.876429</td>\n",
       "      <td>5.454157e-07</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>160000 rows × 12 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             1         2         3         4         5         6         7  \\\n",
       "AAAA -0.270938 -0.944304 -0.227171  0.744803  0.059077 -0.077512 -0.477853   \n",
       "AAAC  0.033789 -0.232603 -0.271458  0.576487  0.035619  0.087608  0.590118   \n",
       "AAAD -0.020398 -0.127749 -0.174455  0.347843  0.142684  0.208679  0.590025   \n",
       "AAAE -0.001018 -0.138712 -0.183161  0.340728  0.121067  0.157871  0.436407   \n",
       "AAAF  0.149717 -0.156524 -0.239304  0.386243  0.103285  0.107756  0.302406   \n",
       "...        ...       ...       ...       ...       ...       ...       ...   \n",
       "YYYS  0.073880  0.038075 -0.097751  0.156184  0.056463  0.074291  0.262512   \n",
       "YYYT -0.091125  0.213370  0.256403  0.246274 -0.086279  0.026923  0.217086   \n",
       "YYYV  0.016488  0.195242  0.216320  0.035269  0.306726  0.025334  0.217759   \n",
       "YYYW  0.134072  0.114107 -0.043856  0.011092  0.076565  0.109907  0.261274   \n",
       "YYYY  0.086278  0.113188 -0.035062  0.017597  0.096670  0.249598  0.261107   \n",
       "\n",
       "             8         9        10  function  stationary_freq  \n",
       "AAAA  0.174491  0.015944  0.052664  0.296301     1.067767e-04  \n",
       "AAAC -0.249005 -0.087750 -0.110291 -2.713474     4.954648e-06  \n",
       "AAAD  0.160819  0.354397  0.676487 -2.912992     4.042194e-06  \n",
       "AAAE  0.195630  0.211100  0.364298 -4.548719     7.619345e-07  \n",
       "AAAF  0.051575  0.171278  0.226772 -3.276738     2.789084e-06  \n",
       "...        ...       ...       ...       ...              ...  \n",
       "YYYS  0.019037  0.144439  0.172686 -4.662925     6.781399e-07  \n",
       "YYYT  0.102111  0.593257  0.003682 -3.223102     2.945947e-06  \n",
       "YYYV -0.028542 -0.038378  0.148356 -3.001718     3.692393e-06  \n",
       "YYYW  0.108909  0.180371  0.365348 -4.723318     6.376209e-07  \n",
       "YYYY  0.108695  0.188331  0.368750 -4.876429     5.454157e-07  \n",
       "\n",
       "[160000 rows x 12 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gb1.nodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "41b00059",
   "metadata": {},
   "outputs": [
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       "6079995  159996  159998\n",
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     "execution_count": 6,
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   "source": [
    "gb1.edges"
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  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "1b0ecac7",
   "metadata": {},
   "outputs": [
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       "    k  decay_rates  relaxation_time\n",
       "0   1     2.554843         0.391413\n",
       "1   2     3.566862         0.280359\n",
       "2   3     4.926568         0.202981\n",
       "3   4     5.023657         0.199058\n",
       "4   5     5.303026         0.188572\n",
       "5   6     5.635594         0.177444\n",
       "6   7     6.294868         0.158860\n",
       "7   8     6.543588         0.152821\n",
       "8   9     6.741685         0.148331\n",
       "9  10     7.000798         0.142841"
      ]
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     "execution_count": 7,
     "metadata": {},
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    "gb1.relaxation_times"
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  {
   "cell_type": "markdown",
   "id": "81525905",
   "metadata": {},
   "source": [
    "## How to build new datasets\n",
    "\n",
    "We also provide functionality to create new datasets and store them in the local copy of your library for easier access. Lets build new datasets from simulated data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "178e64ba",
   "metadata": {},
   "outputs": [
    {
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       "      <td>0.01</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>814 rows × 2 columns</p>\n",
       "</div>"
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      "text/plain": [
       "              y  y_var\n",
       "AAAAA  0.039540   0.01\n",
       "AAAAG -0.117862   0.01\n",
       "AAAAT  0.303257   0.01\n",
       "AAACA  0.230550   0.01\n",
       "AAACC -0.000383   0.01\n",
       "...         ...    ...\n",
       "TTTCT -0.010906   0.01\n",
       "TTTGG -0.398118   0.01\n",
       "TTTTC -0.320779   0.01\n",
       "TTTTG -0.266456   0.01\n",
       "TTTTT -0.141016   0.01\n",
       "\n",
       "[814 rows x 2 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.random.seed(0)\n",
    "lambdas = np.array([10, 2, 0.5, 0.1, 0.02, 0])\n",
    "model = VCregression(seq_length=5, alphabet_type='dna', lambdas=lambdas)\n",
    "data = model.simulate(p_missing=0.2, sigma=0.1).drop('y_true', axis=1).dropna()\n",
    "data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "502e0dfa",
   "metadata": {},
   "source": [
    "The method `build` will use some default values to run Variance Component regression and compute visualization coordinates automatically, but may not be the best choice for any particular dataset."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "de818e53",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 100/100 [00:02<00:00, 41.79it/s]\n"
     ]
    }
   ],
   "source": [
    "test = DataSet('test', data=data)\n",
    "test.build()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "07a8f860",
   "metadata": {},
   "source": [
    "We can now re-load the dataset from disk and verify that it contains the visualization attributes\n",
    "\n",
    "> Note that reinstalling the library will erase the newly created `DataSet`s"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "6c3a1e5b",
   "metadata": {},
   "outputs": [
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       "      <td>0.789508</td>\n",
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       "      <td>-0.919782</td>\n",
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       "      <td>0.320091</td>\n",
       "      <td>0.376623</td>\n",
       "      <td>0.861715</td>\n",
       "      <td>-0.115110</td>\n",
       "      <td>0.965854</td>\n",
       "      <td>0.537670</td>\n",
       "      <td>0.772480</td>\n",
       "      <td>...</td>\n",
       "      <td>2.137501</td>\n",
       "      <td>2.527706</td>\n",
       "      <td>0.950794</td>\n",
       "      <td>1.133436</td>\n",
       "      <td>0.317646</td>\n",
       "      <td>-1.593851</td>\n",
       "      <td>0.628486</td>\n",
       "      <td>-1.566774</td>\n",
       "      <td>-0.120535</td>\n",
       "      <td>0.000020</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAAT</th>\n",
       "      <td>1.960418</td>\n",
       "      <td>2.015446</td>\n",
       "      <td>2.802114</td>\n",
       "      <td>-0.144481</td>\n",
       "      <td>1.141420</td>\n",
       "      <td>2.506787</td>\n",
       "      <td>-1.358454</td>\n",
       "      <td>1.476034</td>\n",
       "      <td>-0.333192</td>\n",
       "      <td>0.398977</td>\n",
       "      <td>...</td>\n",
       "      <td>1.890287</td>\n",
       "      <td>2.614852</td>\n",
       "      <td>2.739016</td>\n",
       "      <td>-0.219729</td>\n",
       "      <td>-0.199154</td>\n",
       "      <td>-1.568183</td>\n",
       "      <td>0.575084</td>\n",
       "      <td>-1.885819</td>\n",
       "      <td>0.220953</td>\n",
       "      <td>0.000543</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACA</th>\n",
       "      <td>3.814800</td>\n",
       "      <td>1.261699</td>\n",
       "      <td>0.811080</td>\n",
       "      <td>4.448437</td>\n",
       "      <td>0.032213</td>\n",
       "      <td>-0.514836</td>\n",
       "      <td>-0.255077</td>\n",
       "      <td>-0.670186</td>\n",
       "      <td>-0.133688</td>\n",
       "      <td>0.566255</td>\n",
       "      <td>...</td>\n",
       "      <td>1.577136</td>\n",
       "      <td>1.222345</td>\n",
       "      <td>-0.527213</td>\n",
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       "      <td>-0.291410</td>\n",
       "      <td>-1.466313</td>\n",
       "      <td>-0.167420</td>\n",
       "      <td>-1.182996</td>\n",
       "      <td>0.201557</td>\n",
       "      <td>0.000450</td>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>TTTGT</th>\n",
       "      <td>2.140434</td>\n",
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       "      <td>0.736442</td>\n",
       "      <td>-0.155903</td>\n",
       "      <td>-0.180521</td>\n",
       "      <td>1.415161</td>\n",
       "      <td>0.583885</td>\n",
       "      <td>0.179762</td>\n",
       "      <td>-0.547157</td>\n",
       "      <td>0.584356</td>\n",
       "      <td>...</td>\n",
       "      <td>0.441516</td>\n",
       "      <td>0.353044</td>\n",
       "      <td>-0.189312</td>\n",
       "      <td>-0.864722</td>\n",
       "      <td>0.205254</td>\n",
       "      <td>0.092788</td>\n",
       "      <td>-0.209753</td>\n",
       "      <td>0.350808</td>\n",
       "      <td>-0.114952</td>\n",
       "      <td>0.000021</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTA</th>\n",
       "      <td>2.902003</td>\n",
       "      <td>0.551990</td>\n",
       "      <td>-0.275240</td>\n",
       "      <td>1.688366</td>\n",
       "      <td>-0.765170</td>\n",
       "      <td>0.558554</td>\n",
       "      <td>0.652595</td>\n",
       "      <td>0.057239</td>\n",
       "      <td>-0.154063</td>\n",
       "      <td>-0.473734</td>\n",
       "      <td>...</td>\n",
       "      <td>0.337019</td>\n",
       "      <td>-0.614797</td>\n",
       "      <td>-0.057125</td>\n",
       "      <td>-0.069688</td>\n",
       "      <td>1.167145</td>\n",
       "      <td>0.828056</td>\n",
       "      <td>-0.541204</td>\n",
       "      <td>1.131136</td>\n",
       "      <td>-0.213529</td>\n",
       "      <td>0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTC</th>\n",
       "      <td>2.601067</td>\n",
       "      <td>0.128646</td>\n",
       "      <td>-0.267689</td>\n",
       "      <td>0.344941</td>\n",
       "      <td>-0.793282</td>\n",
       "      <td>0.625832</td>\n",
       "      <td>0.177349</td>\n",
       "      <td>0.472832</td>\n",
       "      <td>-0.466700</td>\n",
       "      <td>0.047076</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.532616</td>\n",
       "      <td>-0.050942</td>\n",
       "      <td>-0.458822</td>\n",
       "      <td>0.365146</td>\n",
       "      <td>0.399918</td>\n",
       "      <td>0.206811</td>\n",
       "      <td>-0.098076</td>\n",
       "      <td>0.757820</td>\n",
       "      <td>-0.344745</td>\n",
       "      <td>0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTG</th>\n",
       "      <td>2.157413</td>\n",
       "      <td>0.586338</td>\n",
       "      <td>-0.397141</td>\n",
       "      <td>0.210420</td>\n",
       "      <td>-0.676836</td>\n",
       "      <td>0.744688</td>\n",
       "      <td>0.895972</td>\n",
       "      <td>0.421951</td>\n",
       "      <td>0.458642</td>\n",
       "      <td>-0.347510</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.238223</td>\n",
       "      <td>0.093321</td>\n",
       "      <td>0.244368</td>\n",
       "      <td>0.207288</td>\n",
       "      <td>0.372603</td>\n",
       "      <td>0.086408</td>\n",
       "      <td>0.194293</td>\n",
       "      <td>0.455535</td>\n",
       "      <td>-0.283153</td>\n",
       "      <td>0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTT</th>\n",
       "      <td>0.244623</td>\n",
       "      <td>0.310516</td>\n",
       "      <td>0.500102</td>\n",
       "      <td>0.003702</td>\n",
       "      <td>-0.126980</td>\n",
       "      <td>1.207871</td>\n",
       "      <td>0.062054</td>\n",
       "      <td>0.033888</td>\n",
       "      <td>-0.166582</td>\n",
       "      <td>-0.031377</td>\n",
       "      <td>...</td>\n",
       "      <td>0.030637</td>\n",
       "      <td>0.149465</td>\n",
       "      <td>-0.067944</td>\n",
       "      <td>0.222734</td>\n",
       "      <td>0.223881</td>\n",
       "      <td>0.163491</td>\n",
       "      <td>-0.061888</td>\n",
       "      <td>0.205998</td>\n",
       "      <td>-0.090435</td>\n",
       "      <td>0.000027</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1024 rows × 22 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              1         2         3         4         5         6         7  \\\n",
       "AAAAA  2.922532  1.612996  1.922566  1.928836  0.651238  0.724700 -0.626236   \n",
       "AAAAC  2.681952  1.434138  2.081914  0.677991  0.593148  1.109453 -0.824506   \n",
       "AAAAG  2.604061  1.908399  2.159282  0.320091  0.376623  0.861715 -0.115110   \n",
       "AAAAT  1.960418  2.015446  2.802114 -0.144481  1.141420  2.506787 -1.358454   \n",
       "AAACA  3.814800  1.261699  0.811080  4.448437  0.032213 -0.514836 -0.255077   \n",
       "...         ...       ...       ...       ...       ...       ...       ...   \n",
       "TTTGT  2.140434 -0.394854  0.736442 -0.155903 -0.180521  1.415161  0.583885   \n",
       "TTTTA  2.902003  0.551990 -0.275240  1.688366 -0.765170  0.558554  0.652595   \n",
       "TTTTC  2.601067  0.128646 -0.267689  0.344941 -0.793282  0.625832  0.177349   \n",
       "TTTTG  2.157413  0.586338 -0.397141  0.210420 -0.676836  0.744688  0.895972   \n",
       "TTTTT  0.244623  0.310516  0.500102  0.003702 -0.126980  1.207871  0.062054   \n",
       "\n",
       "              8         9        10  ...        13        14        15  \\\n",
       "AAAAA  0.457580 -0.160287  0.765350  ...  2.476916  3.135844  0.294568   \n",
       "AAAAC  1.029326 -0.209692  0.677500  ...  1.768603  2.792991  0.789508   \n",
       "AAAAG  0.965854  0.537670  0.772480  ...  2.137501  2.527706  0.950794   \n",
       "AAAAT  1.476034 -0.333192  0.398977  ...  1.890287  2.614852  2.739016   \n",
       "AAACA -0.670186 -0.133688  0.566255  ...  1.577136  1.222345 -0.527213   \n",
       "...         ...       ...       ...  ...       ...       ...       ...   \n",
       "TTTGT  0.179762 -0.547157  0.584356  ...  0.441516  0.353044 -0.189312   \n",
       "TTTTA  0.057239 -0.154063 -0.473734  ...  0.337019 -0.614797 -0.057125   \n",
       "TTTTC  0.472832 -0.466700  0.047076  ... -0.532616 -0.050942 -0.458822   \n",
       "TTTTG  0.421951  0.458642 -0.347510  ... -0.238223  0.093321  0.244368   \n",
       "TTTTT  0.033888 -0.166582 -0.031377  ...  0.030637  0.149465 -0.067944   \n",
       "\n",
       "             16        17        18        19        20  function  \\\n",
       "AAAAA  1.121940 -0.204409 -1.407941  0.419596 -1.271204 -0.019814   \n",
       "AAAAC  1.052783  0.499965 -1.928383  0.194958 -0.919782 -0.038036   \n",
       "AAAAG  1.133436  0.317646 -1.593851  0.628486 -1.566774 -0.120535   \n",
       "AAAAT -0.219729 -0.199154 -1.568183  0.575084 -1.885819  0.220953   \n",
       "AAACA  0.709598 -0.291410 -1.466313 -0.167420 -1.182996  0.201557   \n",
       "...         ...       ...       ...       ...       ...       ...   \n",
       "TTTGT -0.864722  0.205254  0.092788 -0.209753  0.350808 -0.114952   \n",
       "TTTTA -0.069688  1.167145  0.828056 -0.541204  1.131136 -0.213529   \n",
       "TTTTC  0.365146  0.399918  0.206811 -0.098076  0.757820 -0.344745   \n",
       "TTTTG  0.207288  0.372603  0.086408  0.194293  0.455535 -0.283153   \n",
       "TTTTT  0.222734  0.223881  0.163491 -0.061888  0.205998 -0.090435   \n",
       "\n",
       "       stationary_freq  \n",
       "AAAAA         0.000053  \n",
       "AAAAC         0.000044  \n",
       "AAAAG         0.000020  \n",
       "AAAAT         0.000543  \n",
       "AAACA         0.000450  \n",
       "...                ...  \n",
       "TTTGT         0.000021  \n",
       "TTTTA         0.000008  \n",
       "TTTTC         0.000002  \n",
       "TTTTG         0.000004  \n",
       "TTTTT         0.000027  \n",
       "\n",
       "[1024 rows x 22 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test = DataSet('test')\n",
    "test.nodes"
   ]
  }
 ],
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