make_mutations_subset.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Subset mutations.tsv to top 25 mutations (Table 2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "mutations = pd.read_csv(\"paper/mutations.tsv\", sep=\"\\t\", index_col=0)\n",
    "mutations = mutations[mutations.index <= 25]\n",
    "mutations = mutations[['mutation', 'mean/stddev', 'R / R_A', 'emerged in lineages']]\n",
    "\n",
    "mutations['R / R_A'] = [1 + int(1000 * (x-1)) / 1000.0 for x in mutations['R / R_A']]\n",
    "mutations['emerged in lineages'] = np.array([len(s.split(',')) for s in mutations['emerged in lineages']])\n",
    "mutations['Gene'] = [s.split(':')[0] for s in mutations['mutation']]\n",
    "mutations['Mutation'] = [s.split(':')[1] for s in mutations['mutation']]\n",
    "mutations = mutations[['Gene', 'Mutation', 'R / R_A', 'emerged in lineages']]\n",
    "mutations.columns = ['Gene', 'Mutation', 'Fold increase in transmissibility', 'Number of lineages']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "mutations.to_csv('mutations_subset.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<div>\n",
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       "    .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>Gene</th>\n",
       "      <th>Mutation</th>\n",
       "      <th>Fold increase in transmissibility</th>\n",
       "      <th>Number of lineages</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>rank</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ORF1b</td>\n",
       "      <td>P314L</td>\n",
       "      <td>1.185</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>S</td>\n",
       "      <td>D614G</td>\n",
       "      <td>1.136</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>S</td>\n",
       "      <td>P681H</td>\n",
       "      <td>1.053</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>S</td>\n",
       "      <td>N501Y</td>\n",
       "      <td>1.042</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>S</td>\n",
       "      <td>Y144-</td>\n",
       "      <td>1.028</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ORF8</td>\n",
       "      <td>L84S</td>\n",
       "      <td>1.264</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>S</td>\n",
       "      <td>P681R</td>\n",
       "      <td>1.050</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>ORF1a</td>\n",
       "      <td>D448-</td>\n",
       "      <td>1.352</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>N</td>\n",
       "      <td>S235F</td>\n",
       "      <td>1.024</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ORF1a</td>\n",
       "      <td>G3676-</td>\n",
       "      <td>1.042</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>ORF1a</td>\n",
       "      <td>S3675-</td>\n",
       "      <td>1.041</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>ORF3a</td>\n",
       "      <td>S26L</td>\n",
       "      <td>1.038</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>M</td>\n",
       "      <td>I82T</td>\n",
       "      <td>1.036</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>ORF7a</td>\n",
       "      <td>V82A</td>\n",
       "      <td>1.036</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>S</td>\n",
       "      <td>V70-</td>\n",
       "      <td>1.020</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>N</td>\n",
       "      <td>D3L</td>\n",
       "      <td>1.017</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>N</td>\n",
       "      <td>D377Y</td>\n",
       "      <td>1.044</td>\n",
       "      <td>17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>ORF3a</td>\n",
       "      <td>G251V</td>\n",
       "      <td>1.245</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>ORF8</td>\n",
       "      <td>R52I</td>\n",
       "      <td>1.018</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>S</td>\n",
       "      <td>D950N</td>\n",
       "      <td>1.034</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>ORF1a</td>\n",
       "      <td>T3255I</td>\n",
       "      <td>1.047</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>S</td>\n",
       "      <td>T716I</td>\n",
       "      <td>1.020</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>N</td>\n",
       "      <td>R203M</td>\n",
       "      <td>1.037</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>S</td>\n",
       "      <td>R158G</td>\n",
       "      <td>1.031</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>S</td>\n",
       "      <td>E156-</td>\n",
       "      <td>1.036</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Gene Mutation  Fold increase in transmissibility  Number of lineages\n",
       "rank                                                                       \n",
       "1     ORF1b    P314L                              1.185                   2\n",
       "2         S    D614G                              1.136                   6\n",
       "3         S    P681H                              1.053                  18\n",
       "4         S    N501Y                              1.042                  11\n",
       "5         S    Y144-                              1.028                   6\n",
       "6      ORF8     L84S                              1.264                   1\n",
       "7         S    P681R                              1.050                   8\n",
       "8     ORF1a    D448-                              1.352                  13\n",
       "9         N    S235F                              1.024                   4\n",
       "10    ORF1a   G3676-                              1.042                  12\n",
       "11    ORF1a   S3675-                              1.041                  12\n",
       "12    ORF3a     S26L                              1.038                   2\n",
       "13        M     I82T                              1.036                   7\n",
       "14    ORF7a     V82A                              1.036                   3\n",
       "15        S     V70-                              1.020                   9\n",
       "16        N      D3L                              1.017                   4\n",
       "17        N    D377Y                              1.044                  17\n",
       "18    ORF3a    G251V                              1.245                  15\n",
       "19     ORF8     R52I                              1.018                   2\n",
       "20        S    D950N                              1.034                   3\n",
       "21    ORF1a   T3255I                              1.047                  10\n",
       "22        S    T716I                              1.020                   5\n",
       "23        N    R203M                              1.037                   3\n",
       "24        S    R158G                              1.031                   1\n",
       "25        S    E156-                              1.036                   2"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mutations"
   ]
  }
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