5_characterize_iModulons/5_iModulonDB_setup.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bacillus subtilis Modulome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pymodulon.core import IcaData\n",
    "from pymodulon.io import *\n",
    "from pymodulon.imodulondb import *\n",
    "from pymodulon.util import *\n",
    "import pandas as pd\n",
    "from os import path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "ica_data = load_json_model(path.join('..','data','processed_data','bsu.json.gz'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Table Issues--\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Table</th>\n",
       "      <th>Missing Column</th>\n",
       "      <th>Solution</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>organism</td>\n",
       "      <td>The default, \"New Organism\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>dataset</td>\n",
       "      <td>The default, \"New Dataset\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>strain</td>\n",
       "      <td>The default, \"Unspecified\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>publication_name</td>\n",
       "      <td>The default, \"Unpublished Study\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>publication_link</td>\n",
       "      <td>The publication name will not be a hyperlink.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>gene_link_db</td>\n",
       "      <td>The default, \"External Database\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>organism_folder</td>\n",
       "      <td>The default, \"new_organism\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>dataset_folder</td>\n",
       "      <td>The default, \"new_dataset\", will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Sample</td>\n",
       "      <td>n_replicates</td>\n",
       "      <td>This column will be generated for you.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Sample</td>\n",
       "      <td>doi</td>\n",
       "      <td>Clicking on activity plot bars will not link to relevant papers for the samples.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>name</td>\n",
       "      <td>imodulon_table.index will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>n_genes</td>\n",
       "      <td>This column will be computed for you.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>exp_var</td>\n",
       "      <td>This column will be left blank.</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         Table    Missing Column  \\\n",
       "0   iModulonDB          organism   \n",
       "1   iModulonDB           dataset   \n",
       "2   iModulonDB            strain   \n",
       "3   iModulonDB  publication_name   \n",
       "4   iModulonDB  publication_link   \n",
       "5   iModulonDB      gene_link_db   \n",
       "6   iModulonDB   organism_folder   \n",
       "7   iModulonDB    dataset_folder   \n",
       "8       Sample      n_replicates   \n",
       "9       Sample               doi   \n",
       "10    iModulon              name   \n",
       "11    iModulon           n_genes   \n",
       "12    iModulon           exp_var   \n",
       "\n",
       "                                                                            Solution  \n",
       "0                                         The default, \"New Organism\", will be used.  \n",
       "1                                          The default, \"New Dataset\", will be used.  \n",
       "2                                          The default, \"Unspecified\", will be used.  \n",
       "3                                    The default, \"Unpublished Study\", will be used.  \n",
       "4                                      The publication name will not be a hyperlink.  \n",
       "5                                    The default, \"External Database\", will be used.  \n",
       "6                                         The default, \"new_organism\", will be used.  \n",
       "7                                          The default, \"new_dataset\", will be used.  \n",
       "8                                             This column will be generated for you.  \n",
       "9   Clicking on activity plot bars will not link to relevant papers for the samples.  \n",
       "10                                                imodulon_table.index will be used.  \n",
       "11                                             This column will be computed for you.  \n",
       "12                                                   This column will be left blank.  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--TF Issues--\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>in_trn</th>\n",
       "      <th>has_link</th>\n",
       "      <th>has_gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>S-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>WalR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rex</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fnr</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigM</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EAR riboswitch</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigB</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PyrR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigV</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CodY</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ManR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CymR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>stringent response</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PhoP</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YonO</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TnrA</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YlxR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MtlR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ImmR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigD</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SwrA</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ComA</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigK</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigI</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zur</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thi-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LevR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ComK</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>NusA</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FruR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AcoR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LnrK</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DegU</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Xpf</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Xre</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fur</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CcpA</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CcpN</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>G-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ResD</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigW</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigE</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rok</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GlpP</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MntR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FapR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AbrB</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KipR</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   in_trn has_link has_gene\n",
       "S-box                True    False    False\n",
       "WalR                 True    False     True\n",
       "Rex                  True    False     True\n",
       "Fnr                  True    False     True\n",
       "SigM                 True    False     True\n",
       "EAR riboswitch       True    False    False\n",
       "SigB                 True    False     True\n",
       "PyrR                 True    False     True\n",
       "SigV                 True    False     True\n",
       "CodY                 True    False     True\n",
       "ManR                 True    False     True\n",
       "CymR                 True    False     True\n",
       "stringent response   True    False    False\n",
       "PhoP                 True    False     True\n",
       "YonO                 True    False     True\n",
       "TnrA                 True    False     True\n",
       "YlxR                 True    False    False\n",
       "MtlR                 True    False     True\n",
       "ImmR                 True    False     True\n",
       "SigD                 True    False     True\n",
       "SwrA                 True    False    False\n",
       "ComA                 True    False     True\n",
       "SigK                 True    False    False\n",
       "SigI                 True    False     True\n",
       "Zur                  True    False     True\n",
       "Thi-box              True    False    False\n",
       "LevR                 True    False     True\n",
       "ComK                 True    False     True\n",
       "NusA                 True    False     True\n",
       "FruR                 True    False     True\n",
       "AcoR                 True    False     True\n",
       "LnrK                 True    False    False\n",
       "DegU                 True    False     True\n",
       "Xpf                  True    False     True\n",
       "Xre                  True    False     True\n",
       "Fur                  True    False     True\n",
       "CcpA                 True    False     True\n",
       "CcpN                 True    False     True\n",
       "G-box                True    False    False\n",
       "ResD                 True    False     True\n",
       "SigW                 True    False     True\n",
       "SigE                 True    False     True\n",
       "Rok                  True    False     True\n",
       "GlpP                 True    False     True\n",
       "MntR                 True    False     True\n",
       "FapR                 True    False     True\n",
       "AbrB                 True    False     True\n",
       "KipR                 True    False    False"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Missing Gene Links--\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array(['BSU_00010', 'BSU_00020', 'BSU_00030', ..., 'BSU_41040',\n",
       "       'BSU_41050', 'BSU_41060'], dtype=object)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Missing DOIs--\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array(['SRX8138083', 'SRX8138084', 'SRX8138085', 'SRX8138086',\n",
       "       'SRX8138087', 'SRX8138088', 'ERX4111143', 'ERX4111144',\n",
       "       'ERX4111145', 'ERX4111146', 'ERX4111148', 'ERX4111149',\n",
       "       'ERX4111150', 'ERX4111151', 'ERX4111152', 'ERX4111153',\n",
       "       'ERX4111154', 'ERX4111156', 'ERX4111157', 'ERX4111158',\n",
       "       'SRX5577041', 'SRX5577042', 'SRX5577043', 'SRX5577044',\n",
       "       'SRX5577045', 'SRX5577046', 'SRX5577047', 'SRX5577048',\n",
       "       'SRX5577049', 'SRX5577050', 'SRX5577051', 'SRX5577052',\n",
       "       'SRX5577053', 'SRX5577054', 'SRX5577055', 'SRX5577056',\n",
       "       'SRX5577057', 'SRX5577058', 'SRX5577059', 'SRX5577060',\n",
       "       'SRX5577061', 'SRX5577062', 'SRX5577063', 'SRX5577064',\n",
       "       'SRX5577065', 'SRX5577066', 'SRX5577067', 'SRX5577068',\n",
       "       'SRX533166', 'SRX533171', 'SRX533786', 'SRX533787', 'SRX533789',\n",
       "       'SRX533791', 'SRX533792', 'SRX533793', 'SRX533794', 'SRX533795',\n",
       "       'SRX4703435', 'SRX4703436', 'SRX4703437', 'SRX4703438',\n",
       "       'SRX4703439', 'SRX4703440', 'SRX6902408', 'SRX6902409',\n",
       "       'SRX6902410', 'SRX6902411', 'SRX6902412', 'SRX6902413',\n",
       "       'SRX6902414', 'SRX6902415', 'SRX5278698', 'SRX5278699',\n",
       "       'SRX5278700', 'SRX5278701', 'SRX5278702', 'SRX5278703',\n",
       "       'SRX5278704', 'SRX5278705', 'SRX5278707', 'SRX5278708',\n",
       "       'SRX5278709', 'SRX5278710', 'SRX5278711', 'SRX5278713',\n",
       "       'SRX5278714', 'SRX5278715', 'SRX5278716', 'SRX5278717',\n",
       "       'SRX5278718', 'SRX5278719', 'SRX5278720', 'SRX5278721',\n",
       "       'SRX1254783', 'SRX1254784', 'SRX1254785', 'SRX1254786',\n",
       "       'SRX1473807', 'SRX1473808', 'SRX1473809', 'SRX7520944',\n",
       "       'SRX7520945', 'SRX7520946', 'SRX7520947', 'SRX7520948',\n",
       "       'SRX7520949', 'SRX7520950', 'SRX7520951', 'SRX959206', 'SRX959207',\n",
       "       'SRX959208', 'SRX959209', 'SRX959210', 'SRX959211', 'SRX959212',\n",
       "       'SRX959213', 'SRX959214', 'SRX959215', 'SRX959216', 'SRX959217',\n",
       "       'SRX3269802', 'SRX3269803', 'SRX3269804', 'SRX3269805',\n",
       "       'SRX3269806', 'SRX3269807', 'SRX3269808', 'SRX3269809',\n",
       "       'SRX3269810', 'SRX3269811', 'SRX2529102', 'SRX2529103',\n",
       "       'SRX2529104', 'SRX2529105', 'ERX1981712', 'ERX1981713',\n",
       "       'ERX1981714', 'ERX1981715', 'ERX1981716', 'ERX1981717',\n",
       "       'ERX2274784', 'ERX2274785', 'ERX2274786', 'ERX2274787',\n",
       "       'ERX2274788', 'ERX2274789', 'ERX2274790', 'ERX2274791',\n",
       "       'ERX2274792', 'ERX2274793', 'ERX2274794', 'ERX2274795',\n",
       "       'ERX2274796', 'ERX2274797', 'ERX2274798', 'ERX2274799',\n",
       "       'ERX2274800', 'ERX2274801', 'ERX1819430', 'ERX1819431',\n",
       "       'ERX1819432', 'ERX1819433', 'ERX1819434', 'ERX1819435',\n",
       "       'ERX1819436', 'ERX1819437', 'ERX1819438', 'ERX1819439',\n",
       "       'ERX1819440', 'ERX1819441', 'ERX1819442', 'ERX1819443',\n",
       "       'ERX1819444', 'ERX1819445', 'ERX3440914', 'ERX3440915',\n",
       "       'ERX3440916', 'ERX3440917', 'ERX3440918', 'ERX3440919',\n",
       "       'ERX3440920', 'ERX3440921', 'ERX3440922', 'ERX3440923',\n",
       "       'ERX3440924', 'ERX3440925', 'ERX3440926', 'ERX3440927',\n",
       "       'ERX3440928', 'ERX3440929', 'ERX3440930', 'ERX3440931',\n",
       "       'ERX3440932', 'ERX3440933', 'ERX3440934', 'ERX3440935',\n",
       "       'ERX3440936', 'ERX3440937', 'ERX3440938', 'ERX3440939',\n",
       "       'ERX3440940', 'ERX3440941', 'ERX3440942', 'ERX3440943',\n",
       "       'SRX5347612', 'SRX5347613', 'SRX5347614', 'SRX5347615',\n",
       "       'SRX5347616', 'SRX5347617', 'SRX5347618', 'SRX5347619',\n",
       "       'SRX5347620', 'SRX5347621', 'SRX5347622', 'SRX5347623',\n",
       "       'SRX8170783', 'SRX8170784', 'SRX8170785', 'SRX8170786',\n",
       "       'SRX8170787', 'SRX8170788', 'SRX5177009', 'SRX5177010',\n",
       "       'SRX5177011', 'SRX5177012', 'SRX7354731', 'SRX7354732',\n",
       "       'SRX7354733', 'SRX7354734', 'SRX7354735', 'SRX7354736',\n",
       "       'SRX7354737', 'SRX7354738', 'SRX2508581', 'SRX2508582',\n",
       "       'SRX2508583', 'SRX2508584', 'SRX2508585', 'SRX2508586',\n",
       "       'SRX2508587', 'SRX2508588', 'SRX2508589', 'SRX2508590',\n",
       "       'SRX2508591', 'SRX2508592', 'SRX1736086', 'SRX1736087',\n",
       "       'SRX1736088', 'SRX1736089', 'SRX1736090', 'SRX1736091',\n",
       "       'SRX1736092', 'SRX1736093', 'SRX1736094', 'SRX1736095',\n",
       "       'SRX1736096', 'SRX1736097', 'SRX7176371', 'SRX7176372',\n",
       "       'SRX7176373', 'SRX7176374', 'SRX7176375', 'SRX7176376'],\n",
       "      dtype=object)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "pd.set_option('display.max_colwidth', None)\n",
    "\n",
    "table_issues, tf_issues, missing_gene_links, missing_dois = \\\n",
    "    imodulondb_compatibility(ica_data)\n",
    "\n",
    "print('--Table Issues--')\n",
    "display(table_issues)\n",
    "print('--TF Issues--')\n",
    "display(tf_issues)\n",
    "print('--Missing Gene Links--')\n",
    "display(missing_gene_links.values)\n",
    "print('--Missing DOIs--')\n",
    "display(missing_dois.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add the iModulonDB Table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "ica_data.imodulondb_table  = {\n",
    "     'organism': 'Bacillus subtilis',\n",
    "     'dataset': 'Modulome',\n",
    "     'strain': '168',\n",
    "     'publication_name': 'Sastry, et al., Forthcoming',\n",
    "     'publication_link': '',\n",
    "     'gene_link_db': '<i>Subti</i>Wiki',\n",
    "     'organism_folder': 'b_subtilis',\n",
    "     'dataset_folder': 'modulome'\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add the Explained Variance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "for k in ica_data.imodulon_table.index:\n",
    "    ica_data.imodulon_table.loc[k, 'exp_var'] = explained_variance(\n",
    "        ica_data, imodulons=k)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Rename some iModulon columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "ica_data.imodulon_table = ica_data.imodulon_table.rename({\n",
    "    'category':'broad_category',\n",
    "    'function':'category'\n",
    "    }, axis = 1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Links"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "prefix = 'http://subtiwiki.uni-goettingen.de/v3/gene/search/exact/'\n",
    "\n",
    "# add gene links\n",
    "for g in ica_data.gene_table.index:\n",
    "    ica_data.gene_links[g] = prefix + g\n",
    "\n",
    "# add regulator links\n",
    "for r in tf_issues.index[(tf_issues.has_gene.astype(bool))]:\n",
    "    ica_data.tf_links[r] = prefix + ica_data.name2num(r)\n",
    "    \n",
    "# some regulators don't have genes but do have pages\n",
    "# here, I link to the direct page since I had to check their existence anyway\n",
    "other_regs = {\n",
    "    'SwrA':'http://subtiwiki.uni-goettingen.de/v3/gene/view/5D479874B43F521DB52EDC2C27CDE4967F22DE47',\n",
    "    'SigK':'http://subtiwiki.uni-goettingen.de/v3/gene/view/24F7FD5C7C3A68BB2760ABB8CBD8FBD65E5FF7D4',\n",
    "    'YlxR':'http://subtiwiki.uni-goettingen.de/v3/gene/view/F4097349A563503468A2A14F062AEAC532C7917A',\n",
    "    'LnrK':'http://subtiwiki.uni-goettingen.de/v3/gene/view/387EF370CE24F7A3C20789A57329A02EBED46F53',\n",
    "    'KipR':'http://subtiwiki.uni-goettingen.de/v3/gene/view/7DA9A79876C546B78B716A64706A3A3716018C2E'\n",
    "}\n",
    "for k, v in other_regs.items():\n",
    "    ica_data.tf_links[k] = v"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Sample Table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add replicate numbers\n",
    "for name, group in ica_data.sample_table.groupby(['project', 'condition']):\n",
    "    ica_data.sample_table.loc[group.index, 'replicate'] = range(1, group.shape[0]+1)\n",
    "    \n",
    "# make sample names that include replicate number\n",
    "ica_data.sample_table = ica_data.sample_table.rename({'full_name':'full_condition_name'}, axis = 1)\n",
    "ica_data.sample_table['name'] = \\\n",
    "    ica_data.sample_table.full_condition_name + ':' + \\\n",
    "    ica_data.sample_table.replicate.astype(int).astype(str)\n",
    "\n",
    "# important: adjust naming to this new column\n",
    "ica_data.sample_table = ica_data.sample_table.rename({\n",
    "    'Sample': 'SRS_Sample',\n",
    "    'name': 'sample'\n",
    "    }, axis = 1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "#ica_data.sample_table.to_csv('bsub_sample_table.csv')\n",
    "\n",
    "# TODO \n",
    "# add a DOI column and then replace the existing sample_table"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Double-check Compatibility"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Table Issues--\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Table</th>\n",
       "      <th>Missing Column</th>\n",
       "      <th>Solution</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>iModulonDB</td>\n",
       "      <td>publication_link</td>\n",
       "      <td>The publication name will not be a hyperlink.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Sample</td>\n",
       "      <td>n_replicates</td>\n",
       "      <td>This column will be generated for you.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Sample</td>\n",
       "      <td>doi</td>\n",
       "      <td>Clicking on activity plot bars will not link to relevant papers for the samples.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>name</td>\n",
       "      <td>imodulon_table.index will be used.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>function</td>\n",
       "      <td>The function will be blank in the dataset table and \"Uncharacterized\" in the iModulon dashboard</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>iModulon</td>\n",
       "      <td>n_genes</td>\n",
       "      <td>This column will be computed for you.</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        Table    Missing Column  \\\n",
       "0  iModulonDB  publication_link   \n",
       "1      Sample      n_replicates   \n",
       "2      Sample               doi   \n",
       "3    iModulon              name   \n",
       "4    iModulon          function   \n",
       "5    iModulon           n_genes   \n",
       "\n",
       "                                                                                          Solution  \n",
       "0                                                    The publication name will not be a hyperlink.  \n",
       "1                                                           This column will be generated for you.  \n",
       "2                 Clicking on activity plot bars will not link to relevant papers for the samples.  \n",
       "3                                                               imodulon_table.index will be used.  \n",
       "4  The function will be blank in the dataset table and \"Uncharacterized\" in the iModulon dashboard  \n",
       "5                                                            This column will be computed for you.  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--TF Issues--\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>in_trn</th>\n",
       "      <th>has_link</th>\n",
       "      <th>has_gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>S-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EAR riboswitch</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>stringent response</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>YlxR</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SwrA</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SigK</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thi-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LnrK</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>G-box</th>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KipR</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   in_trn has_link has_gene\n",
       "S-box                True    False    False\n",
       "EAR riboswitch       True    False    False\n",
       "stringent response   True    False    False\n",
       "YlxR                 True     True    False\n",
       "SwrA                 True     True    False\n",
       "SigK                 True     True    False\n",
       "Thi-box              True    False    False\n",
       "LnrK                 True     True    False\n",
       "G-box                True    False    False\n",
       "KipR                 True     True    False"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Missing Gene Links--\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([], dtype=float64)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--Missing DOIs--\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array(['SRX8138083', 'SRX8138084', 'SRX8138085', 'SRX8138086',\n",
       "       'SRX8138087', 'SRX8138088', 'ERX4111143', 'ERX4111144',\n",
       "       'ERX4111145', 'ERX4111146', 'ERX4111148', 'ERX4111149',\n",
       "       'ERX4111150', 'ERX4111151', 'ERX4111152', 'ERX4111153',\n",
       "       'ERX4111154', 'ERX4111156', 'ERX4111157', 'ERX4111158',\n",
       "       'SRX5577041', 'SRX5577042', 'SRX5577043', 'SRX5577044',\n",
       "       'SRX5577045', 'SRX5577046', 'SRX5577047', 'SRX5577048',\n",
       "       'SRX5577049', 'SRX5577050', 'SRX5577051', 'SRX5577052',\n",
       "       'SRX5577053', 'SRX5577054', 'SRX5577055', 'SRX5577056',\n",
       "       'SRX5577057', 'SRX5577058', 'SRX5577059', 'SRX5577060',\n",
       "       'SRX5577061', 'SRX5577062', 'SRX5577063', 'SRX5577064',\n",
       "       'SRX5577065', 'SRX5577066', 'SRX5577067', 'SRX5577068',\n",
       "       'SRX533166', 'SRX533171', 'SRX533786', 'SRX533787', 'SRX533789',\n",
       "       'SRX533791', 'SRX533792', 'SRX533793', 'SRX533794', 'SRX533795',\n",
       "       'SRX4703435', 'SRX4703436', 'SRX4703437', 'SRX4703438',\n",
       "       'SRX4703439', 'SRX4703440', 'SRX6902408', 'SRX6902409',\n",
       "       'SRX6902410', 'SRX6902411', 'SRX6902412', 'SRX6902413',\n",
       "       'SRX6902414', 'SRX6902415', 'SRX5278698', 'SRX5278699',\n",
       "       'SRX5278700', 'SRX5278701', 'SRX5278702', 'SRX5278703',\n",
       "       'SRX5278704', 'SRX5278705', 'SRX5278707', 'SRX5278708',\n",
       "       'SRX5278709', 'SRX5278710', 'SRX5278711', 'SRX5278713',\n",
       "       'SRX5278714', 'SRX5278715', 'SRX5278716', 'SRX5278717',\n",
       "       'SRX5278718', 'SRX5278719', 'SRX5278720', 'SRX5278721',\n",
       "       'SRX1254783', 'SRX1254784', 'SRX1254785', 'SRX1254786',\n",
       "       'SRX1473807', 'SRX1473808', 'SRX1473809', 'SRX7520944',\n",
       "       'SRX7520945', 'SRX7520946', 'SRX7520947', 'SRX7520948',\n",
       "       'SRX7520949', 'SRX7520950', 'SRX7520951', 'SRX959206', 'SRX959207',\n",
       "       'SRX959208', 'SRX959209', 'SRX959210', 'SRX959211', 'SRX959212',\n",
       "       'SRX959213', 'SRX959214', 'SRX959215', 'SRX959216', 'SRX959217',\n",
       "       'SRX3269802', 'SRX3269803', 'SRX3269804', 'SRX3269805',\n",
       "       'SRX3269806', 'SRX3269807', 'SRX3269808', 'SRX3269809',\n",
       "       'SRX3269810', 'SRX3269811', 'SRX2529102', 'SRX2529103',\n",
       "       'SRX2529104', 'SRX2529105', 'ERX1981712', 'ERX1981713',\n",
       "       'ERX1981714', 'ERX1981715', 'ERX1981716', 'ERX1981717',\n",
       "       'ERX2274784', 'ERX2274785', 'ERX2274786', 'ERX2274787',\n",
       "       'ERX2274788', 'ERX2274789', 'ERX2274790', 'ERX2274791',\n",
       "       'ERX2274792', 'ERX2274793', 'ERX2274794', 'ERX2274795',\n",
       "       'ERX2274796', 'ERX2274797', 'ERX2274798', 'ERX2274799',\n",
       "       'ERX2274800', 'ERX2274801', 'ERX1819430', 'ERX1819431',\n",
       "       'ERX1819432', 'ERX1819433', 'ERX1819434', 'ERX1819435',\n",
       "       'ERX1819436', 'ERX1819437', 'ERX1819438', 'ERX1819439',\n",
       "       'ERX1819440', 'ERX1819441', 'ERX1819442', 'ERX1819443',\n",
       "       'ERX1819444', 'ERX1819445', 'ERX3440914', 'ERX3440915',\n",
       "       'ERX3440916', 'ERX3440917', 'ERX3440918', 'ERX3440919',\n",
       "       'ERX3440920', 'ERX3440921', 'ERX3440922', 'ERX3440923',\n",
       "       'ERX3440924', 'ERX3440925', 'ERX3440926', 'ERX3440927',\n",
       "       'ERX3440928', 'ERX3440929', 'ERX3440930', 'ERX3440931',\n",
       "       'ERX3440932', 'ERX3440933', 'ERX3440934', 'ERX3440935',\n",
       "       'ERX3440936', 'ERX3440937', 'ERX3440938', 'ERX3440939',\n",
       "       'ERX3440940', 'ERX3440941', 'ERX3440942', 'ERX3440943',\n",
       "       'SRX5347612', 'SRX5347613', 'SRX5347614', 'SRX5347615',\n",
       "       'SRX5347616', 'SRX5347617', 'SRX5347618', 'SRX5347619',\n",
       "       'SRX5347620', 'SRX5347621', 'SRX5347622', 'SRX5347623',\n",
       "       'SRX8170783', 'SRX8170784', 'SRX8170785', 'SRX8170786',\n",
       "       'SRX8170787', 'SRX8170788', 'SRX5177009', 'SRX5177010',\n",
       "       'SRX5177011', 'SRX5177012', 'SRX7354731', 'SRX7354732',\n",
       "       'SRX7354733', 'SRX7354734', 'SRX7354735', 'SRX7354736',\n",
       "       'SRX7354737', 'SRX7354738', 'SRX2508581', 'SRX2508582',\n",
       "       'SRX2508583', 'SRX2508584', 'SRX2508585', 'SRX2508586',\n",
       "       'SRX2508587', 'SRX2508588', 'SRX2508589', 'SRX2508590',\n",
       "       'SRX2508591', 'SRX2508592', 'SRX1736086', 'SRX1736087',\n",
       "       'SRX1736088', 'SRX1736089', 'SRX1736090', 'SRX1736091',\n",
       "       'SRX1736092', 'SRX1736093', 'SRX1736094', 'SRX1736095',\n",
       "       'SRX1736096', 'SRX1736097', 'SRX7176371', 'SRX7176372',\n",
       "       'SRX7176373', 'SRX7176374', 'SRX7176375', 'SRX7176376'],\n",
       "      dtype=object)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "table_issues, tf_issues, missing_gene_links, missing_dois = \\\n",
    "    imodulondb_compatibility(ica_data)\n",
    "\n",
    "print('--Table Issues--')\n",
    "display(table_issues)\n",
    "print('--TF Issues--')\n",
    "display(tf_issues)\n",
    "print('--Missing Gene Links--')\n",
    "display(missing_gene_links.values)\n",
    "print('--Missing DOIs--')\n",
    "display(missing_dois.values)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Save & Export"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "save_to_json(ica_data, path.join('..','data','processed_data','bsu_imdb.json.gz'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "categories = [\n",
    "    'Carbon Metabolism',\n",
    "    'AA/Nucleotide Metabolism',\n",
    "    'Misc. Metabolism',\n",
    "    'Homeostasis',\n",
    "    'Lifestyles',\n",
    "    'Cellular Processes',\n",
    "    'Stress Response',\n",
    "    'Prophages',\n",
    "    'Other',\n",
    "    'Single Gene',\n",
    "    'Uncharacterized'\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Writing main site files...\n",
      "Done writing main site files. Writing plot files...\n",
      "Two progress bars will appear below. The second will take significantly longer than the first.\n",
      "Writing iModulon page files (1/2)\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "7c42598519ac4bc6887f3c9219ce00bb",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/72 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Writing Gene page files (2/2)\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "e406a7e3793e4588a70a42ac0eb7395e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/4325 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Complete! (Organism = b_subtilis; Dataset = modulome)\n"
     ]
    }
   ],
   "source": [
    "pd.set_option('mode.chained_assignment',None)\n",
    "imodulondb_export(ica_data, '../iModulonDB', cat_order = categories)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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