07.antibiotic_potentiators_table.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "7e64e85a-de23-4240-8c9b-fce7230854b5",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "from collections import defaultdict\n",
    "from copy import deepcopy\n",
    "import time\n",
    "import random\n",
    "from scipy import stats\n",
    "from scipy.stats import mode\n",
    "import seaborn as sns\n",
    "import warnings\n",
    "from collections import defaultdict\n",
    "warnings.filterwarnings(\"ignore\")\n",
    "from scipy.stats import chisquare"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "fb4d5490-085c-4d98-bf93-bea361f3c711",
   "metadata": {},
   "outputs": [],
   "source": [
    "!conda list -e >env.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "512b422e-0884-4607-a1e5-1c3749842bbb",
   "metadata": {},
   "source": [
    "## Extract potentiator hits for all antibiotics\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "a917b7e8-c7e6-4456-9123-e56b03a58053",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Merge sequential and simultaneous hits into a single table\n",
    "\n",
    "all_hits_sequential = pd.read_csv(\"output/04A.pair_annotation/results_allpairs_annotation_withcategories.csv\", index_col=0)\n",
    "all_simultaneous = pd.read_csv(\"output/04B.pair_annotation/results_allpairs_annotation_withcategories.csv\", index_col=0)\n",
    "\n",
    "sequential_merged = all_hits_sequential.merge(all_simultaneous[[\"position_i\", \"position_j\", \"pval_beta_i_on_j\", 'pval_beta_i_on_j_BH_sig']], \n",
    "                                                on=[\"position_i\", \"position_j\"], how=\"left\", suffixes=[\"_sequential\", \"_simultaneous\"])\n",
    "\n",
    "simultaneous_merged = all_simultaneous.merge(all_hits_sequential[[\"position_i\", \"position_j\", \"pval_beta_i_on_j\", 'pval_beta_i_on_j_BH_sig']], \n",
    "                                                on=[\"position_i\", \"position_j\"], how=\"left\", suffixes=[ \"_simultaneous\", \"_sequential\"])\n",
    "\n",
    "all_hits = pd.concat([simultaneous_merged, sequential_merged])\n",
    "all_hits = all_hits.drop_duplicates(subset=[\"position_i\", \"position_j\"]).reset_index(drop=True)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2c5c1db3-2ee1-4daa-9a15-94b0d0240e15",
   "metadata": {
    "tags": []
   },
   "outputs": [
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       "      <td>None</td>\n",
       "      <td>139</td>\n",
       "      <td>5</td>\n",
       "      <td>602</td>\n",
       "      <td>60683</td>\n",
       "      <td>137</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.492056e-20</td>\n",
       "      <td>True</td>\n",
       "      <td>371.576279</td>\n",
       "      <td>137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>578670</th>\n",
       "      <td>474630</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>2030489</td>\n",
       "      <td>esxM</td>\n",
       "      <td>786</td>\n",
       "      <td>6</td>\n",
       "      <td>3817</td>\n",
       "      <td>4727</td>\n",
       "      <td>110</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>4.856003e-10</td>\n",
       "      <td>True</td>\n",
       "      <td>538.883662</td>\n",
       "      <td>110</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527055</th>\n",
       "      <td>36832</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>1096633</td>\n",
       "      <td>None</td>\n",
       "      <td>107</td>\n",
       "      <td>5</td>\n",
       "      <td>523</td>\n",
       "      <td>60683</td>\n",
       "      <td>105</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.352732e-09</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>105</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52011</th>\n",
       "      <td>38459</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>2030355</td>\n",
       "      <td>esxM</td>\n",
       "      <td>786</td>\n",
       "      <td>78</td>\n",
       "      <td>3817</td>\n",
       "      <td>5112</td>\n",
       "      <td>101</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>8.057993e-06</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48209</th>\n",
       "      <td>12995</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>3136335</td>\n",
       "      <td>None</td>\n",
       "      <td>786</td>\n",
       "      <td>314</td>\n",
       "      <td>3817</td>\n",
       "      <td>7632</td>\n",
       "      <td>91</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>7.921586e-01</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46594</th>\n",
       "      <td>3129</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>2123169</td>\n",
       "      <td>None</td>\n",
       "      <td>786</td>\n",
       "      <td>184</td>\n",
       "      <td>3817</td>\n",
       "      <td>2876</td>\n",
       "      <td>86</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>1.092388e-13</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72461</th>\n",
       "      <td>120062</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>4385937</td>\n",
       "      <td>Rv3900c</td>\n",
       "      <td>786</td>\n",
       "      <td>14</td>\n",
       "      <td>3817</td>\n",
       "      <td>3531</td>\n",
       "      <td>92</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>6.099387e-11</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>93</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52861</th>\n",
       "      <td>43395</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>3527974</td>\n",
       "      <td>PPE53</td>\n",
       "      <td>786</td>\n",
       "      <td>26</td>\n",
       "      <td>3817</td>\n",
       "      <td>3905</td>\n",
       "      <td>91</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.578778e-08</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>92</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>573399</th>\n",
       "      <td>433304</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>1094472</td>\n",
       "      <td>None</td>\n",
       "      <td>786</td>\n",
       "      <td>172</td>\n",
       "      <td>3817</td>\n",
       "      <td>2328</td>\n",
       "      <td>82</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>4.915686e-17</td>\n",
       "      <td>True</td>\n",
       "      <td>385.718587</td>\n",
       "      <td>83</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53271</th>\n",
       "      <td>44979</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>2300546</td>\n",
       "      <td>pks12</td>\n",
       "      <td>786</td>\n",
       "      <td>193</td>\n",
       "      <td>3817</td>\n",
       "      <td>7351</td>\n",
       "      <td>73</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>9.975742e-01</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>82</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>569903</th>\n",
       "      <td>419133</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>1094538</td>\n",
       "      <td>None</td>\n",
       "      <td>786</td>\n",
       "      <td>263</td>\n",
       "      <td>3817</td>\n",
       "      <td>2258</td>\n",
       "      <td>77</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>3.077141e-15</td>\n",
       "      <td>True</td>\n",
       "      <td>387.700851</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55551</th>\n",
       "      <td>58319</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>4247429</td>\n",
       "      <td>embB</td>\n",
       "      <td>786</td>\n",
       "      <td>865</td>\n",
       "      <td>3817</td>\n",
       "      <td>2866</td>\n",
       "      <td>11</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>EMB,EMB,EMB</td>\n",
       "      <td>True</td>\n",
       "      <td>EMB</td>\n",
       "      <td>between_known_AB</td>\n",
       "      <td>9.999955e-01</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>577261</th>\n",
       "      <td>455387</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>1468150</td>\n",
       "      <td>None</td>\n",
       "      <td>786</td>\n",
       "      <td>64</td>\n",
       "      <td>3817</td>\n",
       "      <td>2194</td>\n",
       "      <td>74</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>3.040646e-14</td>\n",
       "      <td>True</td>\n",
       "      <td>319.658785</td>\n",
       "      <td>74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75002</th>\n",
       "      <td>141005</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>2338994</td>\n",
       "      <td>Rv2082</td>\n",
       "      <td>107</td>\n",
       "      <td>19</td>\n",
       "      <td>523</td>\n",
       "      <td>32513</td>\n",
       "      <td>71</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.410574e-06</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527486</th>\n",
       "      <td>44546</td>\n",
       "      <td>1674048</td>\n",
       "      <td>fabG1</td>\n",
       "      <td>1340208</td>\n",
       "      <td>PPE18</td>\n",
       "      <td>139</td>\n",
       "      <td>30</td>\n",
       "      <td>602</td>\n",
       "      <td>21626</td>\n",
       "      <td>71</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>1.022386e-07</td>\n",
       "      <td>True</td>\n",
       "      <td>525.274815</td>\n",
       "      <td>71</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57380</th>\n",
       "      <td>61260</td>\n",
       "      <td>1673425</td>\n",
       "      <td>None</td>\n",
       "      <td>4247431</td>\n",
       "      <td>embB</td>\n",
       "      <td>786</td>\n",
       "      <td>821</td>\n",
       "      <td>3817</td>\n",
       "      <td>2090</td>\n",
       "      <td>10</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>EMB,EMB,EMB</td>\n",
       "      <td>True</td>\n",
       "      <td>EMB</td>\n",
       "      <td>between_known_AB</td>\n",
       "      <td>9.993510e-01</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>68</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527722</th>\n",
       "      <td>48592</td>\n",
       "      <td>1674048</td>\n",
       "      <td>fabG1</td>\n",
       "      <td>340132</td>\n",
       "      <td>PPE3</td>\n",
       "      <td>139</td>\n",
       "      <td>150</td>\n",
       "      <td>602</td>\n",
       "      <td>21827</td>\n",
       "      <td>67</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>1.273452e-05</td>\n",
       "      <td>True</td>\n",
       "      <td>578.433293</td>\n",
       "      <td>67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45598</th>\n",
       "      <td>475</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>2155168</td>\n",
       "      <td>katG</td>\n",
       "      <td>107</td>\n",
       "      <td>2098</td>\n",
       "      <td>523</td>\n",
       "      <td>12564</td>\n",
       "      <td>49</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>INH,INH,INH,INH,INH</td>\n",
       "      <td>True</td>\n",
       "      <td>INH</td>\n",
       "      <td>between_known_AB</td>\n",
       "      <td>2.550422e-13</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>66</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47443</th>\n",
       "      <td>8369</td>\n",
       "      <td>1674048</td>\n",
       "      <td>fabG1</td>\n",
       "      <td>2122395</td>\n",
       "      <td>lldD2</td>\n",
       "      <td>139</td>\n",
       "      <td>277</td>\n",
       "      <td>602</td>\n",
       "      <td>19900</td>\n",
       "      <td>60</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.096023e-04</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527506</th>\n",
       "      <td>44880</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>1340208</td>\n",
       "      <td>PPE18</td>\n",
       "      <td>107</td>\n",
       "      <td>30</td>\n",
       "      <td>523</td>\n",
       "      <td>21626</td>\n",
       "      <td>61</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.513795e-10</td>\n",
       "      <td>True</td>\n",
       "      <td>527.981856</td>\n",
       "      <td>61</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527742</th>\n",
       "      <td>48941</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>340132</td>\n",
       "      <td>PPE3</td>\n",
       "      <td>107</td>\n",
       "      <td>150</td>\n",
       "      <td>523</td>\n",
       "      <td>21827</td>\n",
       "      <td>60</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>2.124449e-09</td>\n",
       "      <td>True</td>\n",
       "      <td>591.460788</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47444</th>\n",
       "      <td>8427</td>\n",
       "      <td>1673432</td>\n",
       "      <td>None</td>\n",
       "      <td>2122395</td>\n",
       "      <td>lldD2</td>\n",
       "      <td>107</td>\n",
       "      <td>277</td>\n",
       "      <td>523</td>\n",
       "      <td>19900</td>\n",
       "      <td>58</td>\n",
       "      <td>...</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>False</td>\n",
       "      <td>NaN</td>\n",
       "      <td>known_AB_second</td>\n",
       "      <td>4.065884e-10</td>\n",
       "      <td>True</td>\n",
       "      <td>NaN</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>40 rows × 39 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Unnamed: 0  position_i gene_name_i  position_j gene_name_j  \\\n",
       "527021       36273     1673425        None     1096633        None   \n",
       "528636       63830     1673425        None     2338994      Rv2082   \n",
       "527474       44432     1673425        None     1340208       PPE18   \n",
       "527709       48467     1673425        None      340132        PPE3   \n",
       "46692         5321     1673425        None     3883626      Rv3466   \n",
       "587432      577848     1673425        None     2338990      Rv2082   \n",
       "55276        57354     1673425        None     3446699      Rv3081   \n",
       "72583       120996     1673425        None     1722228        pks5   \n",
       "48537        15793     1673425        None     3730411       PPE54   \n",
       "589346      609374     1673425        None     1533583       PPE19   \n",
       "586001      555361     1673425        None     3895247       PPE60   \n",
       "580319      483946     1673425        None     2626105        esxO   \n",
       "54885        55524     1673425        None     2030521        esxM   \n",
       "47420         7999     1673425        None     3336528        None   \n",
       "585645      549271     1673425        None      154191        None   \n",
       "583116      507922     1673425        None     2240062        None   \n",
       "587263      574961     1673425        None       50557        ino1   \n",
       "45352          211     1673425        None     2155168        katG   \n",
       "527035       36420     1674048       fabG1     1096633        None   \n",
       "578670      474630     1673425        None     2030489        esxM   \n",
       "527055       36832     1673432        None     1096633        None   \n",
       "52011        38459     1673425        None     2030355        esxM   \n",
       "48209        12995     1673425        None     3136335        None   \n",
       "46594         3129     1673425        None     2123169        None   \n",
       "72461       120062     1673425        None     4385937     Rv3900c   \n",
       "52861        43395     1673425        None     3527974       PPE53   \n",
       "573399      433304     1673425        None     1094472        None   \n",
       "53271        44979     1673425        None     2300546       pks12   \n",
       "569903      419133     1673425        None     1094538        None   \n",
       "55551        58319     1673425        None     4247429        embB   \n",
       "577261      455387     1673425        None     1468150        None   \n",
       "75002       141005     1673432        None     2338994      Rv2082   \n",
       "527486       44546     1674048       fabG1     1340208       PPE18   \n",
       "57380        61260     1673425        None     4247431        embB   \n",
       "527722       48592     1674048       fabG1      340132        PPE3   \n",
       "45598          475     1673432        None     2155168        katG   \n",
       "47443         8369     1674048       fabG1     2122395       lldD2   \n",
       "527506       44880     1673432        None     1340208       PPE18   \n",
       "527742       48941     1673432        None      340132        PPE3   \n",
       "47444         8427     1673432        None     2122395       lldD2   \n",
       "\n",
       "        n_mutations_i  n_mutations_j  n_branches_with_i  n_branches_with_j  \\\n",
       "527021            786              5               3817              60683   \n",
       "528636            786             19               3817              32513   \n",
       "527474            786             30               3817              21626   \n",
       "527709            786            150               3817              21827   \n",
       "46692             786            469               3817              19374   \n",
       "587432            786             18               3817              16336   \n",
       "55276             786             83               3817              16441   \n",
       "72583             786             13               3817              16173   \n",
       "48537             786            369               3817              15646   \n",
       "589346            786            116               3817              10743   \n",
       "586001            786             10               3817               6699   \n",
       "580319            786             13               3817               5959   \n",
       "54885             786             69               3817               6159   \n",
       "47420             786            116               3817               6246   \n",
       "585645            786             25               3817               6689   \n",
       "583116            786              5               3817               5611   \n",
       "587263            786             16               3817               9463   \n",
       "45352             786           2098               3817              12564   \n",
       "527035            139              5                602              60683   \n",
       "578670            786              6               3817               4727   \n",
       "527055            107              5                523              60683   \n",
       "52011             786             78               3817               5112   \n",
       "48209             786            314               3817               7632   \n",
       "46594             786            184               3817               2876   \n",
       "72461             786             14               3817               3531   \n",
       "52861             786             26               3817               3905   \n",
       "573399            786            172               3817               2328   \n",
       "53271             786            193               3817               7351   \n",
       "569903            786            263               3817               2258   \n",
       "55551             786            865               3817               2866   \n",
       "577261            786             64               3817               2194   \n",
       "75002             107             19                523              32513   \n",
       "527486            139             30                602              21626   \n",
       "57380             786            821               3817               2090   \n",
       "527722            139            150                602              21827   \n",
       "45598             107           2098                523              12564   \n",
       "47443             139            277                602              19900   \n",
       "527506            107             30                523              21626   \n",
       "527742            107            150                523              21827   \n",
       "47444             107            277                523              19900   \n",
       "\n",
       "        n_muts_i_on_branch_j  ...  in_antigen_protein_j  \\\n",
       "527021                   768  ...                 False   \n",
       "528636                   491  ...                 False   \n",
       "527474                   376  ...                  True   \n",
       "527709                   318  ...                  True   \n",
       "46692                    307  ...                 False   \n",
       "587432                   282  ...                 False   \n",
       "55276                    207  ...                 False   \n",
       "72583                    209  ...                 False   \n",
       "48537                    194  ...                  True   \n",
       "589346                   181  ...                  True   \n",
       "586001                   178  ...                  True   \n",
       "580319                   178  ...                  True   \n",
       "54885                    177  ...                 False   \n",
       "47420                    173  ...                 False   \n",
       "585645                   174  ...                 False   \n",
       "583116                   170  ...                 False   \n",
       "587263                   164  ...                 False   \n",
       "45352                     90  ...                  True   \n",
       "527035                   137  ...                 False   \n",
       "578670                   110  ...                 False   \n",
       "527055                   105  ...                 False   \n",
       "52011                    101  ...                 False   \n",
       "48209                     91  ...                 False   \n",
       "46594                     86  ...                 False   \n",
       "72461                     92  ...                 False   \n",
       "52861                     91  ...                 False   \n",
       "573399                    82  ...                 False   \n",
       "53271                     73  ...                 False   \n",
       "569903                    77  ...                 False   \n",
       "55551                     11  ...                 False   \n",
       "577261                    74  ...                 False   \n",
       "75002                     71  ...                 False   \n",
       "527486                    71  ...                  True   \n",
       "57380                     10  ...                 False   \n",
       "527722                    67  ...                  True   \n",
       "45598                     49  ...                  True   \n",
       "47443                     60  ...                  True   \n",
       "527506                    61  ...                  True   \n",
       "527742                    60  ...                  True   \n",
       "47444                     58  ...                  True   \n",
       "\n",
       "        in_known_ABR_position_j         known_drug_j  in_possible_ABR_gene_j  \\\n",
       "527021                    False                  NaN                   False   \n",
       "528636                    False                  NaN                   False   \n",
       "527474                    False                  NaN                   False   \n",
       "527709                    False                  NaN                   False   \n",
       "46692                     False                  NaN                   False   \n",
       "587432                    False                  NaN                   False   \n",
       "55276                     False                  NaN                   False   \n",
       "72583                     False                  NaN                   False   \n",
       "48537                     False                  NaN                   False   \n",
       "589346                    False                  NaN                   False   \n",
       "586001                    False                  NaN                   False   \n",
       "580319                    False                  NaN                   False   \n",
       "54885                     False                  NaN                   False   \n",
       "47420                     False                  NaN                   False   \n",
       "585645                    False                  NaN                   False   \n",
       "583116                    False                  NaN                   False   \n",
       "587263                    False                  NaN                   False   \n",
       "45352                      True  INH,INH,INH,INH,INH                    True   \n",
       "527035                    False                  NaN                   False   \n",
       "578670                    False                  NaN                   False   \n",
       "527055                    False                  NaN                   False   \n",
       "52011                     False                  NaN                   False   \n",
       "48209                     False                  NaN                   False   \n",
       "46594                     False                  NaN                   False   \n",
       "72461                     False                  NaN                   False   \n",
       "52861                     False                  NaN                   False   \n",
       "573399                    False                  NaN                   False   \n",
       "53271                     False                  NaN                   False   \n",
       "569903                    False                  NaN                   False   \n",
       "55551                      True          EMB,EMB,EMB                    True   \n",
       "577261                    False                  NaN                   False   \n",
       "75002                     False                  NaN                   False   \n",
       "527486                    False                  NaN                   False   \n",
       "57380                      True          EMB,EMB,EMB                    True   \n",
       "527722                    False                  NaN                   False   \n",
       "45598                      True  INH,INH,INH,INH,INH                    True   \n",
       "47443                     False                  NaN                   False   \n",
       "527506                    False                  NaN                   False   \n",
       "527742                    False                  NaN                   False   \n",
       "47444                     False                  NaN                   False   \n",
       "\n",
       "        possible_drug_j        annotation  pval_beta_i_on_j_sequential  \\\n",
       "527021              NaN   known_AB_second                 7.839476e-28   \n",
       "528636              NaN   known_AB_second                 1.226391e-19   \n",
       "527474              NaN   known_AB_second                 3.146643e-22   \n",
       "527709              NaN   known_AB_second                 1.889911e-05   \n",
       "46692               NaN   known_AB_second                 2.470575e-08   \n",
       "587432              NaN   known_AB_second                 2.197887e-13   \n",
       "55276               NaN   known_AB_second                 4.914138e-01   \n",
       "72583               NaN   known_AB_second                 2.981139e-01   \n",
       "48537               NaN   known_AB_second                 4.264086e-01   \n",
       "589346              NaN   known_AB_second                 1.493815e-07   \n",
       "586001              NaN   known_AB_second                 1.007475e-25   \n",
       "580319              NaN   known_AB_second                 3.777188e-30   \n",
       "54885               NaN   known_AB_second                 1.995826e-30   \n",
       "47420               NaN   known_AB_second                 3.059820e-25   \n",
       "585645              NaN   known_AB_second                 3.889570e-22   \n",
       "583116              NaN   known_AB_second                 2.725001e-29   \n",
       "587263              NaN   known_AB_second                 9.313409e-08   \n",
       "45352               INH  between_known_AB                 1.000000e+00   \n",
       "527035              NaN   known_AB_second                 2.492056e-20   \n",
       "578670              NaN   known_AB_second                 4.856003e-10   \n",
       "527055              NaN   known_AB_second                 2.352732e-09   \n",
       "52011               NaN   known_AB_second                 8.057993e-06   \n",
       "48209               NaN   known_AB_second                 7.921586e-01   \n",
       "46594               NaN   known_AB_second                 1.092388e-13   \n",
       "72461               NaN   known_AB_second                 6.099387e-11   \n",
       "52861               NaN   known_AB_second                 2.578778e-08   \n",
       "573399              NaN   known_AB_second                 4.915686e-17   \n",
       "53271               NaN   known_AB_second                 9.975742e-01   \n",
       "569903              NaN   known_AB_second                 3.077141e-15   \n",
       "55551               EMB  between_known_AB                 9.999955e-01   \n",
       "577261              NaN   known_AB_second                 3.040646e-14   \n",
       "75002               NaN   known_AB_second                 2.410574e-06   \n",
       "527486              NaN   known_AB_second                 1.022386e-07   \n",
       "57380               EMB  between_known_AB                 9.993510e-01   \n",
       "527722              NaN   known_AB_second                 1.273452e-05   \n",
       "45598               INH  between_known_AB                 2.550422e-13   \n",
       "47443               NaN   known_AB_second                 2.096023e-04   \n",
       "527506              NaN   known_AB_second                 2.513795e-10   \n",
       "527742              NaN   known_AB_second                 2.124449e-09   \n",
       "47444               NaN   known_AB_second                 4.065884e-10   \n",
       "\n",
       "       pval_beta_i_on_j_BH_sig_sequential  median_distance  num_dependent  \n",
       "527021                               True       590.477720            768  \n",
       "528636                               True       619.327023            491  \n",
       "527474                               True       559.401902            377  \n",
       "527709                               True       568.675319            321  \n",
       "46692                                True              NaN            316  \n",
       "587432                               True       769.046309            282  \n",
       "55276                               False              NaN            214  \n",
       "72583                               False              NaN            212  \n",
       "48537                               False              NaN            211  \n",
       "589346                               True       603.102116            186  \n",
       "586001                               True       789.894490            178  \n",
       "580319                               True       789.894490            178  \n",
       "54885                                True              NaN            178  \n",
       "47420                                True              NaN            175  \n",
       "585645                               True       790.333318            174  \n",
       "583116                               True       654.513863            170  \n",
       "587263                               True       613.208632            165  \n",
       "45352                               False              NaN            149  \n",
       "527035                               True       371.576279            137  \n",
       "578670                               True       538.883662            110  \n",
       "527055                               True              NaN            105  \n",
       "52011                                True              NaN            103  \n",
       "48209                               False              NaN            103  \n",
       "46594                                True              NaN             94  \n",
       "72461                                True              NaN             93  \n",
       "52861                                True              NaN             92  \n",
       "573399                               True       385.718587             83  \n",
       "53271                               False              NaN             82  \n",
       "569903                               True       387.700851             79  \n",
       "55551                               False              NaN             77  \n",
       "577261                               True       319.658785             74  \n",
       "75002                                True              NaN             72  \n",
       "527486                               True       525.274815             71  \n",
       "57380                               False              NaN             68  \n",
       "527722                               True       578.433293             67  \n",
       "45598                                True              NaN             66  \n",
       "47443                                True              NaN             63  \n",
       "527506                               True       527.981856             61  \n",
       "527742                               True       591.460788             60  \n",
       "47444                                True              NaN             59  \n",
       "\n",
       "[40 rows x 39 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "known_antibiotic_first = all_hits.dropna(subset=[\"known_drug_i\"]).query(\"pval_beta_i_on_j_BH_sig_sequential or pval_beta_i_on_j_BH_sig_simultaneous\")\n",
    "\n",
    "known_antibiotic_first['num_dependent'] = known_antibiotic_first.n_muts_i_on_branch_j + known_antibiotic_first.n_muts_same_branch\n",
    "know_ab_first = known_antibiotic_first.loc[known_antibiotic_first.possible_drug_i.isnull(), :]\n",
    "know_ab_first.sort_values('num_dependent', ascending=False).head(40)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "eef7949c-fc61-47ad-aa93-2856efad3d7e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "5246\n"
     ]
    }
   ],
   "source": [
    "def _process_known_hits(input_list):\n",
    "    \"\"\"\n",
    "    splits the possible associated drugs (string separated by ,) into a list\n",
    "    \"\"\"\n",
    "    output_list = []\n",
    "    for item in input_list:\n",
    "        #print(item)\n",
    "        if type(item) != str:\n",
    "            output_list.append(np.nan)\n",
    "        else:\n",
    "            splitted = item.split(\",\")\n",
    "            exclusive= list(set(splitted))\n",
    "            output_list.append(exclusive)\n",
    "    return output_list\n",
    "\n",
    "## Note! This is code recycling, actually the table contains hits where the known antibiotic resistance mutation was second\n",
    "known_antibiotic_first = all_hits.dropna(subset=[\"known_drug_i\"]).query(\"pval_beta_i_on_j_BH_sig_sequential or pval_beta_i_on_j_BH_sig_simultaneous\")\n",
    "\n",
    "known_antibiotic_first[\"known_drug_i\"] = _process_known_hits(known_antibiotic_first.known_drug_i)\n",
    "known_antibiotic_first[\"possible_drug_i\"] = _process_known_hits(known_antibiotic_first.possible_drug_i)\n",
    "\n",
    "known_antibiotic_first[\"known_drug_j\"] = _process_known_hits(known_antibiotic_first.known_drug_j)\n",
    "known_antibiotic_first[\"possible_drug_j\"] = _process_known_hits(known_antibiotic_first.possible_drug_j)\n",
    "\n",
    "print(len(known_antibiotic_first))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c9917889-1006-4883-9a23-cdd3c497f6da",
   "metadata": {},
   "outputs": [],
   "source": [
    "between_antibiotic_indices = []\n",
    "antibiotic_indices = []\n",
    "\n",
    "known_antibiotic_first[\"within_same_drug\"] = False\n",
    "\n",
    "for idx, row in known_antibiotic_first.iterrows():\n",
    "    \n",
    "    set_of_known_first = set(row.known_drug_i)\n",
    "    set_of_known_second = set()\n",
    "    known_drug_second = False\n",
    "    \n",
    "    if type(row.known_drug_j) is list:\n",
    "        set_of_known_second= set(row.known_drug_j)\n",
    "        known_drug_second = True\n",
    "        \n",
    "    elif type(row.possible_drug_j) is list:\n",
    "        set_of_known_second= set(row.possible_drug_j)\n",
    "        known_drug_second = True\n",
    "        \n",
    "    if not known_drug_second:\n",
    "        antibiotic_indices.append(idx)\n",
    "    \n",
    "    elif len(set_of_known_first.intersection(set_of_known_second)) > 0:\n",
    "        antibiotic_indices.append(idx)\n",
    "        known_antibiotic_first.loc[idx, \"within_same_drug\"] = True\n",
    "        \n",
    "    else:\n",
    "        between_antibiotic_indices.append(idx)\n",
    "        \n",
    "between_antibiotic_hits = known_antibiotic_first.loc[between_antibiotic_indices]\n",
    "antibiotic_hits = known_antibiotic_first.loc[antibiotic_indices]\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "87d07b62-5fe3-42f1-a77d-7ed04033d3bf",
   "metadata": {},
   "source": [
    "## Compute per-drug output tables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "6f2c9bf1-24f6-46bf-955e-67422e094ae0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ETH 209\n",
      "EMB 348\n",
      "LZD 221\n",
      "LEV 358\n",
      "AMI 424\n",
      "KAN 417\n",
      "RIF 581\n",
      "INH 153\n",
      "MXF 358\n",
      "CAP 246\n",
      "STM 497\n",
      "PZA 1230\n"
     ]
    }
   ],
   "source": [
    "## These will contain all hits except the between-antibiotic hits\n",
    "\n",
    "## First get the list of all names of drugs in the dataset\n",
    "drug_list = []\n",
    "for idx, row in antibiotic_hits.iterrows():\n",
    "    drugs1 = row.possible_drug_i\n",
    "    drugs2 = row.possible_drug_j\n",
    "    \n",
    "    if type(drugs1) != list:\n",
    "        drugs1= []\n",
    "    if type(drugs2) != list:\n",
    "        drugs2=[]\n",
    "    \n",
    "    for drug in drugs1 + drugs2:\n",
    "        drug_list.append(drug)\n",
    "\n",
    "drug_list = list(set(drug_list))\n",
    "\n",
    "## Then create an empty df for each\n",
    "df_dict = {drug:pd.DataFrame() for drug in drug_list}\n",
    "\n",
    "## now concatenate each row to the appropriate drug dataframe\n",
    "for idx, row in antibiotic_hits.iterrows():\n",
    "    drugs1 = row.possible_drug_i\n",
    "    drugs2 = row.possible_drug_j\n",
    "    \n",
    "    if type(drugs1) != list:\n",
    "        drugs1= []\n",
    "    if type(drugs2) != list:\n",
    "        drugs2=[]\n",
    "    \n",
    "    for drug in drugs1:\n",
    "        df_dict[drug] = df_dict[drug].append(row)\n",
    "        \n",
    "    for drug in drugs2:\n",
    "        df_dict[drug] = df_dict[drug].append(row)\n",
    "        \n",
    "for drug, df in df_dict.items():\n",
    "    print(drug, len(df))\n",
    "    df.sort_values(\"n_muts_i_on_branch_j\", ascending=False).to_csv(f\"output/05.antibiotic/{drug}_potentiator_antibiotic_hits.csv\")\n",
    "    df.query(\"pval_beta_i_on_j_BH_sig_sequential != 0\").query(\"pval_beta_i_on_j_BH_sig_sequential\").sort_values(\n",
    "        \"n_muts_i_on_branch_j\", ascending=False\n",
    "    ).to_csv(f\"output/05.antibiotic/{drug}_potentiator_antibiotic_hits_sequential.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4934d536-45b9-4f2e-ba94-e501eea1634a",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "83ea0740-32f2-4a43-8731-716d3d95ef6c",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f6dd2734-2fb6-4d46-95db-5e3f21bfeb5d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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