{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "be5d3b4f",
   "metadata": {},
   "source": [
    "# Datasets\n",
    "\n",
    "In this section, we illustrate the built-in datasets that are used for demonstration of the library throughout the documentation and how to build and store new datasets to make them conveniently and locally accessible with the same interface.\n",
    "\n",
    "Datasets consist of complete combinatorial landscapes that can be visualized and analyzed, as well as the data from which they were derived. Both the inference of the complete landscape and the calculation of visualization coordinates are precomputed to provide quick access to the various layers of interest."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6b281ef0",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import required libraries\n",
    "import numpy as np\n",
    "import pandas as pd\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",
       "    .dataframe tbody tr th:only-of-type {\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",
       "    </tr>\n",
       "    <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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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <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>1</th>\n",
       "      <th>2</th>\n",
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       "      <th>4</th>\n",
       "      <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",
       "      <td>0.296301</td>\n",
       "      <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"
   ]
  },
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   "cell_type": "code",
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       "              i       j\n",
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       "...         ...     ...\n",
       "6079995  159996  159998\n",
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       "6079997  159997  159998\n",
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       "\n",
       "[6080000 rows x 2 columns]"
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     "execution_count": 6,
     "metadata": {},
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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"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
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    "gb1.relaxation_times"
   ]
  },
  {
   "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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       "  </tbody>\n",
       "</table>\n",
       "<p>816 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              y  y_var\n",
       "AAAAA  0.425225   0.01\n",
       "AAAAC  0.025961   0.01\n",
       "AAAAG  0.211691   0.01\n",
       "AAAAT -0.169990   0.01\n",
       "AAACA  0.141775   0.01\n",
       "...         ...    ...\n",
       "TTTGA  0.080597   0.01\n",
       "TTTGC -0.092545   0.01\n",
       "TTTGG -0.509507   0.01\n",
       "TTTTA  0.510968   0.01\n",
       "TTTTG -0.646299   0.01\n",
       "\n",
       "[816 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",
    "f, X, y, y_var = model.simulate(p_missing=0.2, y_var=0.01)\n",
    "data = pd.DataFrame({'y': y, 'y_var': y_var}, index=X)\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, 42.60it/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>-0.123224</td>\n",
       "      <td>-0.889849</td>\n",
       "      <td>0.905356</td>\n",
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       "      <td>0.049589</td>\n",
       "      <td>-0.813528</td>\n",
       "      <td>-0.733640</td>\n",
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       "      <td>0.185295</td>\n",
       "      <td>0.014557</td>\n",
       "      <td>0.233692</td>\n",
       "      <td>0.093785</td>\n",
       "      <td>0.387054</td>\n",
       "      <td>1.734146e-04</td>\n",
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       "      <th>AAAAC</th>\n",
       "      <td>1.072408</td>\n",
       "      <td>0.056435</td>\n",
       "      <td>2.945652</td>\n",
       "      <td>0.570610</td>\n",
       "      <td>-0.548389</td>\n",
       "      <td>0.499496</td>\n",
       "      <td>-0.060271</td>\n",
       "      <td>0.210738</td>\n",
       "      <td>0.454159</td>\n",
       "      <td>0.315377</td>\n",
       "      <td>...</td>\n",
       "      <td>0.027614</td>\n",
       "      <td>0.182956</td>\n",
       "      <td>0.041282</td>\n",
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       "      <td>0.012360</td>\n",
       "      <td>-0.103109</td>\n",
       "      <td>0.145002</td>\n",
       "      <td>0.012005</td>\n",
       "      <td>0.079653</td>\n",
       "      <td>4.783712e-06</td>\n",
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       "      <td>-0.424879</td>\n",
       "      <td>-0.173879</td>\n",
       "      <td>1.601030</td>\n",
       "      <td>0.393521</td>\n",
       "      <td>-0.376543</td>\n",
       "      <td>0.198026</td>\n",
       "      <td>0.068529</td>\n",
       "      <td>0.023428</td>\n",
       "      <td>-0.521934</td>\n",
       "      <td>-0.191951</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.087000</td>\n",
       "      <td>-0.027370</td>\n",
       "      <td>-0.045159</td>\n",
       "      <td>0.083975</td>\n",
       "      <td>-0.047376</td>\n",
       "      <td>-0.036584</td>\n",
       "      <td>0.109612</td>\n",
       "      <td>0.077264</td>\n",
       "      <td>0.242677</td>\n",
       "      <td>3.211605e-05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAAAT</th>\n",
       "      <td>1.638025</td>\n",
       "      <td>-0.526015</td>\n",
       "      <td>0.963103</td>\n",
       "      <td>0.227400</td>\n",
       "      <td>-0.480507</td>\n",
       "      <td>0.580577</td>\n",
       "      <td>0.149562</td>\n",
       "      <td>-0.231371</td>\n",
       "      <td>-0.251046</td>\n",
       "      <td>0.174849</td>\n",
       "      <td>...</td>\n",
       "      <td>0.201388</td>\n",
       "      <td>-0.116860</td>\n",
       "      <td>0.107007</td>\n",
       "      <td>0.044851</td>\n",
       "      <td>0.242405</td>\n",
       "      <td>-0.009095</td>\n",
       "      <td>0.133066</td>\n",
       "      <td>0.010694</td>\n",
       "      <td>-0.130124</td>\n",
       "      <td>4.127115e-07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACA</th>\n",
       "      <td>2.029814</td>\n",
       "      <td>0.478617</td>\n",
       "      <td>1.541410</td>\n",
       "      <td>1.394887</td>\n",
       "      <td>-0.103456</td>\n",
       "      <td>0.165921</td>\n",
       "      <td>2.445179</td>\n",
       "      <td>0.035222</td>\n",
       "      <td>-0.144542</td>\n",
       "      <td>0.367994</td>\n",
       "      <td>...</td>\n",
       "      <td>0.299338</td>\n",
       "      <td>-0.400981</td>\n",
       "      <td>-0.294678</td>\n",
       "      <td>1.177327</td>\n",
       "      <td>0.726800</td>\n",
       "      <td>0.021389</td>\n",
       "      <td>0.309360</td>\n",
       "      <td>0.199590</td>\n",
       "      <td>0.133852</td>\n",
       "      <td>9.009335e-06</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>TTTGT</th>\n",
       "      <td>3.332679</td>\n",
       "      <td>1.524216</td>\n",
       "      <td>-0.882499</td>\n",
       "      <td>-0.696858</td>\n",
       "      <td>0.836397</td>\n",
       "      <td>-1.156986</td>\n",
       "      <td>0.556218</td>\n",
       "      <td>0.500014</td>\n",
       "      <td>0.156163</td>\n",
       "      <td>0.216689</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.609086</td>\n",
       "      <td>0.306015</td>\n",
       "      <td>0.283575</td>\n",
       "      <td>0.606585</td>\n",
       "      <td>0.218290</td>\n",
       "      <td>-0.430605</td>\n",
       "      <td>1.027785</td>\n",
       "      <td>0.702348</td>\n",
       "      <td>-0.115364</td>\n",
       "      <td>4.903661e-07</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTA</th>\n",
       "      <td>2.298655</td>\n",
       "      <td>-0.360357</td>\n",
       "      <td>-0.505533</td>\n",
       "      <td>1.352307</td>\n",
       "      <td>6.025070</td>\n",
       "      <td>0.182953</td>\n",
       "      <td>0.533421</td>\n",
       "      <td>-0.309203</td>\n",
       "      <td>0.471387</td>\n",
       "      <td>0.024318</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.550174</td>\n",
       "      <td>0.808017</td>\n",
       "      <td>-0.201772</td>\n",
       "      <td>1.759322</td>\n",
       "      <td>0.725695</td>\n",
       "      <td>-0.542566</td>\n",
       "      <td>2.092282</td>\n",
       "      <td>3.031618</td>\n",
       "      <td>0.390967</td>\n",
       "      <td>1.815254e-04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTC</th>\n",
       "      <td>2.684310</td>\n",
       "      <td>1.833576</td>\n",
       "      <td>0.192108</td>\n",
       "      <td>-0.550983</td>\n",
       "      <td>1.460191</td>\n",
       "      <td>0.469683</td>\n",
       "      <td>0.416367</td>\n",
       "      <td>0.345825</td>\n",
       "      <td>1.089355</td>\n",
       "      <td>-0.056080</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.101757</td>\n",
       "      <td>0.570731</td>\n",
       "      <td>0.027791</td>\n",
       "      <td>1.139062</td>\n",
       "      <td>-0.095064</td>\n",
       "      <td>-0.590156</td>\n",
       "      <td>1.184556</td>\n",
       "      <td>0.822767</td>\n",
       "      <td>-0.252124</td>\n",
       "      <td>9.926395e-08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTG</th>\n",
       "      <td>1.489311</td>\n",
       "      <td>-0.156888</td>\n",
       "      <td>-0.669274</td>\n",
       "      <td>0.185673</td>\n",
       "      <td>1.648772</td>\n",
       "      <td>0.578333</td>\n",
       "      <td>0.343027</td>\n",
       "      <td>0.667288</td>\n",
       "      <td>0.128079</td>\n",
       "      <td>-0.152963</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.138289</td>\n",
       "      <td>0.307081</td>\n",
       "      <td>-0.010085</td>\n",
       "      <td>0.994944</td>\n",
       "      <td>0.112638</td>\n",
       "      <td>-0.182646</td>\n",
       "      <td>0.764041</td>\n",
       "      <td>0.776003</td>\n",
       "      <td>-0.557506</td>\n",
       "      <td>2.803548e-09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTTT</th>\n",
       "      <td>2.870706</td>\n",
       "      <td>-0.490323</td>\n",
       "      <td>-1.859482</td>\n",
       "      <td>0.103815</td>\n",
       "      <td>0.915930</td>\n",
       "      <td>1.053966</td>\n",
       "      <td>0.071009</td>\n",
       "      <td>0.573608</td>\n",
       "      <td>0.114060</td>\n",
       "      <td>0.178955</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.906039</td>\n",
       "      <td>0.441809</td>\n",
       "      <td>0.200234</td>\n",
       "      <td>0.844890</td>\n",
       "      <td>0.371698</td>\n",
       "      <td>-0.195801</td>\n",
       "      <td>1.786632</td>\n",
       "      <td>1.891382</td>\n",
       "      <td>0.064394</td>\n",
       "      <td>4.002759e-06</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  1.179083 -0.268895  3.019227  0.931148 -0.423071  0.313136  0.423140   \n",
       "AAAAC  1.072408  0.056435  2.945652  0.570610 -0.548389  0.499496 -0.060271   \n",
       "AAAAG -0.424879 -0.173879  1.601030  0.393521 -0.376543  0.198026  0.068529   \n",
       "AAAAT  1.638025 -0.526015  0.963103  0.227400 -0.480507  0.580577  0.149562   \n",
       "AAACA  2.029814  0.478617  1.541410  1.394887 -0.103456  0.165921  2.445179   \n",
       "...         ...       ...       ...       ...       ...       ...       ...   \n",
       "TTTGT  3.332679  1.524216 -0.882499 -0.696858  0.836397 -1.156986  0.556218   \n",
       "TTTTA  2.298655 -0.360357 -0.505533  1.352307  6.025070  0.182953  0.533421   \n",
       "TTTTC  2.684310  1.833576  0.192108 -0.550983  1.460191  0.469683  0.416367   \n",
       "TTTTG  1.489311 -0.156888 -0.669274  0.185673  1.648772  0.578333  0.343027   \n",
       "TTTTT  2.870706 -0.490323 -1.859482  0.103815  0.915930  1.053966  0.071009   \n",
       "\n",
       "              8         9        10  ...        13        14        15  \\\n",
       "AAAAA -0.123224 -0.889849  0.905356  ...  0.049589 -0.813528 -0.733640   \n",
       "AAAAC  0.210738  0.454159  0.315377  ...  0.027614  0.182956  0.041282   \n",
       "AAAAG  0.023428 -0.521934 -0.191951  ... -0.087000 -0.027370 -0.045159   \n",
       "AAAAT -0.231371 -0.251046  0.174849  ...  0.201388 -0.116860  0.107007   \n",
       "AAACA  0.035222 -0.144542  0.367994  ...  0.299338 -0.400981 -0.294678   \n",
       "...         ...       ...       ...  ...       ...       ...       ...   \n",
       "TTTGT  0.500014  0.156163  0.216689  ... -0.609086  0.306015  0.283575   \n",
       "TTTTA -0.309203  0.471387  0.024318  ... -0.550174  0.808017 -0.201772   \n",
       "TTTTC  0.345825  1.089355 -0.056080  ... -0.101757  0.570731  0.027791   \n",
       "TTTTG  0.667288  0.128079 -0.152963  ... -0.138289  0.307081 -0.010085   \n",
       "TTTTT  0.573608  0.114060  0.178955  ... -0.906039  0.441809  0.200234   \n",
       "\n",
       "             16        17        18        19        20  function  \\\n",
       "AAAAA  0.179086  0.185295  0.014557  0.233692  0.093785  0.387054   \n",
       "AAAAC  0.196853  0.012360 -0.103109  0.145002  0.012005  0.079653   \n",
       "AAAAG  0.083975 -0.047376 -0.036584  0.109612  0.077264  0.242677   \n",
       "AAAAT  0.044851  0.242405 -0.009095  0.133066  0.010694 -0.130124   \n",
       "AAACA  1.177327  0.726800  0.021389  0.309360  0.199590  0.133852   \n",
       "...         ...       ...       ...       ...       ...       ...   \n",
       "TTTGT  0.606585  0.218290 -0.430605  1.027785  0.702348 -0.115364   \n",
       "TTTTA  1.759322  0.725695 -0.542566  2.092282  3.031618  0.390967   \n",
       "TTTTC  1.139062 -0.095064 -0.590156  1.184556  0.822767 -0.252124   \n",
       "TTTTG  0.994944  0.112638 -0.182646  0.764041  0.776003 -0.557506   \n",
       "TTTTT  0.844890  0.371698 -0.195801  1.786632  1.891382  0.064394   \n",
       "\n",
       "       stationary_freq  \n",
       "AAAAA     1.734146e-04  \n",
       "AAAAC     4.783712e-06  \n",
       "AAAAG     3.211605e-05  \n",
       "AAAAT     4.127115e-07  \n",
       "AAACA     9.009335e-06  \n",
       "...                ...  \n",
       "TTTGT     4.903661e-07  \n",
       "TTTTA     1.815254e-04  \n",
       "TTTTC     9.926395e-08  \n",
       "TTTTG     2.803548e-09  \n",
       "TTTTT     4.002759e-06  \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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