constellation_analysis.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "2d638474-a388-4ece-ba20-c4e9b2765004",
   "metadata": {},
   "source": [
    "# Overview on the spike mutations on the different lineages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 175,
   "id": "f0961cb1-f0cf-416c-905f-cab5424bb20d",
   "metadata": {},
   "outputs": [
    {
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       "[(0.00392156862745098, 0.45098039215686275, 0.6980392156862745),\n",
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       " (0.33725490196078434, 0.7058823529411765, 0.9137254901960784)]"
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     "execution_count": 175,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "import os\n",
    "import re\n",
    "import json\n",
    "import glob\n",
    "import time\n",
    "from Bio.Alphabet import ProteinAlphabet\n",
    "from logzero import logger\n",
    "import pandas as pd\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib.patches as mpatches\n",
    "import numpy as np\n",
    "from upsetplot import UpSet\n",
    "import gtfparse\n",
    "\n",
    "sns.set_style(\"whitegrid\")\n",
    "sns.set_context(\"notebook\")\n",
    "sns.color_palette(\"colorblind\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 174,
   "id": "b4e6c0cc-74d5-4479-98d2-4b17523be898",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "pip freeze > constellation_analysis.requirements.txt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0afb2956-4168-422d-be0c-eccd8bf1e33a",
   "metadata": {},
   "source": [
    "## Data loading\n",
    "\n",
    "The lineages data comes from this repository https://github.com/cov-lineages/constellations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 272,
   "id": "4a683265-4cd8-4de3-bfcd-4e0659f9cbfd",
   "metadata": {},
   "outputs": [],
   "source": [
    "data_folder = \"resources/constellations/constellations/definitions\"\n",
    "figures_folder = \"figures/constellations\"\n",
    "gtf_file = \"resources/Sars_cov_2.ASM985889v3.101.gtf\"\n",
    "dpi = 200"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 244,
   "id": "60924cee-1813-4ff5-ada1-59646fb5a44a",
   "metadata": {},
   "outputs": [
    {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nsp3:L741F</td>\n",
       "      <td>A.23.1</td>\n",
       "      <td>None</td>\n",
       "      <td>nsp3</td>\n",
       "      <td>L741F</td>\n",
       "      <td>741.0</td>\n",
       "      <td>L</td>\n",
       "      <td>F</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>nsp6:M86I</td>\n",
       "      <td>A.23.1</td>\n",
       "      <td>None</td>\n",
       "      <td>nsp6</td>\n",
       "      <td>M86I</td>\n",
       "      <td>86.0</td>\n",
       "      <td>M</td>\n",
       "      <td>I</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>nsp6:L98F</td>\n",
       "      <td>A.23.1</td>\n",
       "      <td>None</td>\n",
       "      <td>nsp6</td>\n",
       "      <td>L98F</td>\n",
       "      <td>98.0</td>\n",
       "      <td>L</td>\n",
       "      <td>F</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>nsp6:M183I</td>\n",
       "      <td>A.23.1</td>\n",
       "      <td>None</td>\n",
       "      <td>nsp6</td>\n",
       "      <td>M183I</td>\n",
       "      <td>183.0</td>\n",
       "      <td>M</td>\n",
       "      <td>I</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>S:R102I</td>\n",
       "      <td>A.23.1</td>\n",
       "      <td>None</td>\n",
       "      <td>S</td>\n",
       "      <td>R102I</td>\n",
       "      <td>102.0</td>\n",
       "      <td>R</td>\n",
       "      <td>I</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "        sites lineage parent_lineage protein mutation  position reference  \\\n",
       "0  nsp3:L741F  A.23.1           None    nsp3    L741F     741.0         L   \n",
       "1   nsp6:M86I  A.23.1           None    nsp6     M86I      86.0         M   \n",
       "2   nsp6:L98F  A.23.1           None    nsp6     L98F      98.0         L   \n",
       "3  nsp6:M183I  A.23.1           None    nsp6    M183I     183.0         M   \n",
       "4     S:R102I  A.23.1           None       S    R102I     102.0         R   \n",
       "\n",
       "  alternate  \n",
       "0         F  \n",
       "1         I  \n",
       "2         F  \n",
       "3         I  \n",
       "4         I  "
      ]
     },
     "execution_count": 244,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mutation_pattern = re.compile('([A-Z\\-]+)([0-9]+)([A-Z\\-]+)')\n",
    "\n",
    "def parse_mutation(mutation, protein):\n",
    "    reference = None\n",
    "    position = None\n",
    "    alternate = None\n",
    "    if protein == \"del\":\n",
    "        # del:28248:6\n",
    "        values = mutation.split(\":\")\n",
    "        if len(values) > 1:\n",
    "            position = int(values[1])\n",
    "    else:\n",
    "        # S:R102I\n",
    "        match = mutation_pattern.match(mutation.split(\":\")[1]) \n",
    "        if match:\n",
    "            reference = match.group(1)\n",
    "            position = int(match.group(2))\n",
    "            alternate = match.group(3)\n",
    "    return reference, position, alternate\n",
    "    \n",
    "\n",
    "lineages_tmp = {}\n",
    "lineages_with_parent_tmp = []\n",
    "p = re.compile('([A-Z\\-]+)([0-9]+)([A-Z\\-]+)')\n",
    "for f in os.listdir(data_folder):\n",
    "    if f.endswith(\".json\"):\n",
    "        lineage = f.strip(\".json\")\n",
    "        data = json.load(open(os.path.join(data_folder, f)))\n",
    "        lineage = pd.DataFrame(data.get(\"sites\"), columns=[\"sites\"])\n",
    "        lineage_name = data.get(\"variant\").get(\"mrca_lineage\")\n",
    "        if lineage_name is None or lineage_name == 'None':\n",
    "            lineage_name = data.get(\"variant\").get(\"lineage_name\")\n",
    "        lineage[\"lineage\"] = lineage_name\n",
    "        parent_lineage = data.get(\"variant\").get(\"parent_lineage\")\n",
    "        lineage[\"parent_lineage\"] = parent_lineage\n",
    "        lineage[\"protein\"] = lineage.sites.transform(lambda l: l.split(\":\")[0])\n",
    "        lineage[\"mutation\"] = lineage.sites.transform(lambda l: str(l.split(\":\")[1]))\n",
    "        lineage[\"position\"] = lineage[[\"sites\", \"protein\"]].apply(lambda m: parse_mutation(mutation=m[0], protein=m[1])[1], axis=1)\n",
    "        lineage[\"reference\"] = lineage[[\"sites\", \"protein\"]].apply(lambda m: parse_mutation(mutation=m[0], protein=m[1])[0], axis=1)\n",
    "        lineage[\"alternate\"] = lineage[[\"sites\", \"protein\"]].apply(lambda m: parse_mutation(mutation=m[0], protein=m[1])[2], axis=1)\n",
    "        has_parent = parent_lineage is not None and parent_lineage != \"None\"\n",
    "        if has_parent:\n",
    "            lineages_with_parent_tmp.append(lineage)\n",
    "        else:\n",
    "            lineages_tmp[lineage_name] = lineage\n",
    "\n",
    "# builds lineages having a parent... only one level inheritance is supported, AY.4.2 which has two levels is the only exception\n",
    "for l in lineages_with_parent_tmp:\n",
    "    lineage_name = l.lineage.head(1)[0]\n",
    "    if lineage_name != \"AY.4.2\":\n",
    "        parent_lineage_template = lineages_tmp.get(l.parent_lineage.head(1)[0]).copy(deep=True)\n",
    "        parent_lineage_template.lineage = lineage_name\n",
    "        joint_lineage = pd.concat([l, parent_lineage_template])\n",
    "        lineages_tmp[lineage_name] = joint_lineage\n",
    "    else:\n",
    "        ay42_lineage = l\n",
    "\n",
    "# builds inherited mutations into AY.4.2 only when AY.4 has already been built\n",
    "parent_lineage_template = lineages_tmp.get(\"AY.4\").copy(deep=True)\n",
    "parent_lineage_template.lineage = \"AY.4.2\"\n",
    "joint_lineage = pd.concat([ay42_lineage, parent_lineage_template])\n",
    "lineages_tmp[\"AY.4.2\"] = joint_lineage\n",
    "\n",
    "\n",
    "lineages = pd.concat(lineages_tmp.values())\n",
    "lineages.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "id": "52e01125-bdca-4d7e-91f7-7dfda90b7833",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['A.23.1', 'B.1.617.3', 'C.37', 'B.1.1.318', 'B.1.621', 'B.1.526',\n",
       "       'B.1.617.2', 'B.1.427', 'B.1.617.1', 'B.1.1.7', 'AV.1', 'B.1.525',\n",
       "       'P.2', 'B.1.351', 'B.1.1.529', 'P.1', 'B.1.429', 'P.3', 'BA.1',\n",
       "       'BA.3', 'BA.2', 'AY.4', 'AY.4.2'], dtype=object)"
      ]
     },
     "execution_count": 112,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# all lineages\n",
    "lineages.lineage.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "id": "3e76a651-6437-446c-a354-8f5e2cfea8b6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['A.23.1', 'B.1.617.3', 'C.37', 'B.1.1.318', 'B.1.621', 'B.1.526',\n",
       "       'B.1.617.2', 'B.1.427', 'B.1.617.1', 'B.1.1.7', 'AV.1', 'B.1.525',\n",
       "       'P.2', 'B.1.351', 'B.1.1.529', 'P.1', 'B.1.429', 'P.3', 'BA.1',\n",
       "       'BA.3', 'BA.2', 'AY.4'], dtype=object)"
      ]
     },
     "execution_count": 113,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# lineages without a parent\n",
    "lineages[lineages.parent_lineage.isna()].lineage.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "id": "e07b1626-6d2a-492f-9f57-4d7f4cab46aa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['BA.1', 'BA.3', 'BA.2', 'AY.4', 'AY.4.2'], dtype=object)"
      ]
     },
     "execution_count": 114,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# lineages with a parent\n",
    "lineages[~lineages.parent_lineage.isna()].lineage.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 116,
   "id": "750e3071-b963-43b2-88e9-f09e86798d45",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['B.1.1.529', 'B.1.617.2', 'AY.4'], dtype=object)"
      ]
     },
     "execution_count": 116,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# lineages with sons (or daughters...)\n",
    "lineages[~lineages.parent_lineage.isna()].parent_lineage.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 165,
   "id": "f173cf3c-4816-45d8-b5bb-32999a467b62",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['nsp3', 'nsp6', 'S', 'ORF8', 'N', 'nuc', 'nsp5', 'ORF7a', 'ORF1a',\n",
       "       'ORF1b', 'nsp4', 'del', 'nsp15', 'M', 'spike', 'ORF3a', '1ab',\n",
       "       'orf1a', 'orf1b', 'orf3a', 'n', 'nsp13', 's', '8', 'nsp12', 'E',\n",
       "       'ORF1ab', 'NSP2', 'orf1ab', 'e', 'm', 'nsp7', 'orf6'], dtype=object)"
      ]
     },
     "execution_count": 165,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages.protein.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 191,
   "id": "a38136a9-f1b2-4816-81f7-f7651f3a2391",
   "metadata": {},
   "outputs": [
    {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>seqname</th>\n",
       "      <th>source</th>\n",
       "      <th>feature</th>\n",
       "      <th>start</th>\n",
       "      <th>end</th>\n",
       "      <th>score</th>\n",
       "      <th>strand</th>\n",
       "      <th>frame</th>\n",
       "      <th>attribute</th>\n",
       "      <th>gene_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MN908947.3</td>\n",
       "      <td>ensembl</td>\n",
       "      <td>gene</td>\n",
       "      <td>266</td>\n",
       "      <td>21555</td>\n",
       "      <td>NaN</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>gene_id \"ENSSASG00005000002\"; gene_version \"1\"...</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MN908947.3</td>\n",
       "      <td>ensembl</td>\n",
       "      <td>transcript</td>\n",
       "      <td>266</td>\n",
       "      <td>21555</td>\n",
       "      <td>NaN</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>gene_id \"ENSSASG00005000002\"; gene_version \"1\"...</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>MN908947.3</td>\n",
       "      <td>ensembl</td>\n",
       "      <td>exon</td>\n",
       "      <td>266</td>\n",
       "      <td>21555</td>\n",
       "      <td>NaN</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>gene_id \"ENSSASG00005000002\"; gene_version \"1\"...</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MN908947.3</td>\n",
       "      <td>ensembl</td>\n",
       "      <td>CDS</td>\n",
       "      <td>266</td>\n",
       "      <td>21552</td>\n",
       "      <td>NaN</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>gene_id \"ENSSASG00005000002\"; gene_version \"1\"...</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>MN908947.3</td>\n",
       "      <td>ensembl</td>\n",
       "      <td>start_codon</td>\n",
       "      <td>266</td>\n",
       "      <td>268</td>\n",
       "      <td>NaN</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>gene_id \"ENSSASG00005000002\"; gene_version \"1\"...</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      seqname   source      feature  start    end  score strand frame  \\\n",
       "0  MN908947.3  ensembl         gene    266  21555    NaN      +     0   \n",
       "1  MN908947.3  ensembl   transcript    266  21555    NaN      +     0   \n",
       "2  MN908947.3  ensembl         exon    266  21555    NaN      +     0   \n",
       "3  MN908947.3  ensembl          CDS    266  21552    NaN      +     0   \n",
       "4  MN908947.3  ensembl  start_codon    266    268    NaN      +     0   \n",
       "\n",
       "                                           attribute gene_name  \n",
       "0  gene_id \"ENSSASG00005000002\"; gene_version \"1\"...    ORF1ab  \n",
       "1  gene_id \"ENSSASG00005000002\"; gene_version \"1\"...    ORF1ab  \n",
       "2  gene_id \"ENSSASG00005000002\"; gene_version \"1\"...    ORF1ab  \n",
       "3  gene_id \"ENSSASG00005000002\"; gene_version \"1\"...    ORF1ab  \n",
       "4  gene_id \"ENSSASG00005000002\"; gene_version \"1\"...    ORF1ab  "
      ]
     },
     "execution_count": 191,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gtf = gtfparse.parse_gtf(gtf_file)\n",
    "gtf[\"gene_name\"] = gtf.attribute.transform(lambda x: x.split(\"gene_name \")[1].strip(\"\\\"\").split(\"\\\";\")[0])\n",
    "gtf.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 193,
   "id": "cc2b0516-68fb-44bb-bf35-497c8f211333",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\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_name</th>\n",
       "      <th>start</th>\n",
       "      <th>end</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ORF1ab</td>\n",
       "      <td>266</td>\n",
       "      <td>21555</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ORF1ab</td>\n",
       "      <td>266</td>\n",
       "      <td>13483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>S</td>\n",
       "      <td>21563</td>\n",
       "      <td>25384</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>ORF3a</td>\n",
       "      <td>25393</td>\n",
       "      <td>26220</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>E</td>\n",
       "      <td>26245</td>\n",
       "      <td>26472</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>M</td>\n",
       "      <td>26523</td>\n",
       "      <td>27191</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>ORF6</td>\n",
       "      <td>27202</td>\n",
       "      <td>27387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>ORF7a</td>\n",
       "      <td>27394</td>\n",
       "      <td>27759</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>ORF7b</td>\n",
       "      <td>27756</td>\n",
       "      <td>27887</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>ORF8</td>\n",
       "      <td>27894</td>\n",
       "      <td>28259</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>N</td>\n",
       "      <td>28274</td>\n",
       "      <td>29533</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>66</th>\n",
       "      <td>ORF10</td>\n",
       "      <td>29558</td>\n",
       "      <td>29674</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   gene_name  start    end\n",
       "0     ORF1ab    266  21555\n",
       "6     ORF1ab    266  13483\n",
       "12         S  21563  25384\n",
       "18     ORF3a  25393  26220\n",
       "24         E  26245  26472\n",
       "30         M  26523  27191\n",
       "36      ORF6  27202  27387\n",
       "42     ORF7a  27394  27759\n",
       "48     ORF7b  27756  27887\n",
       "54      ORF8  27894  28259\n",
       "60         N  28274  29533\n",
       "66     ORF10  29558  29674"
      ]
     },
     "execution_count": 193,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gene_coordinates = gtf[gtf.feature == \"gene\"][[\"gene_name\", \"start\", \"end\"]]\n",
    "gene_coordinates"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c87caf92-2d8b-49dd-8fd6-919dfd2257b6",
   "metadata": {},
   "source": [
    "## Data normalization"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "11b25cf5-32d8-43ea-9812-0ab0eff244d3",
   "metadata": {},
   "source": [
    "### Protein names\n",
    "\n",
    "There are some synonyms used for the proteins, eg: spike, S and s. These are normalised here.\n",
    "\n",
    "Also, all the domains from protein ORF1ab are just considered as ORF1ab; and separate ORF1a and ORF1b are considered as ORF1ab.\n",
    "\n",
    "### Mutation representation\n",
    "\n",
    "Mutations are represented mostly in the protein space, but there are some exceptions that are represented in genomic coordinates. \n",
    "* Synonymous mutations are represented as nuc:A27259C and we are missing the corresponding protein annotation. In this example the mutations occurs in the ORF6 and its representation in the protein space would be R20R.\n",
    "* Some deletions are represented as del:28362:9 and we are also missing the corresponding protein annotations.\n",
    "\n",
    "We will manually annotate the overlapped proteins using a GTF reference file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 246,
   "id": "7303f8fc-a742-48b7-9434-c117f2033fca",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\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>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nuc:C835T</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C835T</td>\n",
       "      <td>835.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>nuc:C16293T</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C16293T</td>\n",
       "      <td>16293.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>nuc:T27384C</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>T27384C</td>\n",
       "      <td>27384.0</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nuc:C3961T</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C3961T</td>\n",
       "      <td>3961.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>del:11287:9</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>11287</td>\n",
       "      <td>11287.0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>del:28248:6</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>28248</td>\n",
       "      <td>28248.0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>nuc:C8986T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C8986T</td>\n",
       "      <td>8986.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>nuc:A11332G</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>A11332G</td>\n",
       "      <td>11332.0</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>nuc:C27874T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C27874T</td>\n",
       "      <td>27874.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>nuc:G29742T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>G29742T</td>\n",
       "      <td>29742.0</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>132 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          sites    lineage parent_lineage protein mutation  position  \\\n",
       "0     nuc:C835T  B.1.617.3           None     nuc    C835T     835.0   \n",
       "5   nuc:C16293T  B.1.617.3           None     nuc  C16293T   16293.0   \n",
       "11  nuc:T27384C  B.1.617.3           None     nuc  T27384C   27384.0   \n",
       "0    nuc:C3961T  B.1.1.318           None     nuc   C3961T    3961.0   \n",
       "5   del:11287:9  B.1.1.318           None     del    11287   11287.0   \n",
       "..          ...        ...            ...     ...      ...       ...   \n",
       "2   del:28248:6     AY.4.2      B.1.617.2     del    28248   28248.0   \n",
       "7    nuc:C8986T     AY.4.2      B.1.617.2     nuc   C8986T    8986.0   \n",
       "11  nuc:A11332G     AY.4.2      B.1.617.2     nuc  A11332G   11332.0   \n",
       "16  nuc:C27874T     AY.4.2      B.1.617.2     nuc  C27874T   27874.0   \n",
       "18  nuc:G29742T     AY.4.2      B.1.617.2     nuc  G29742T   29742.0   \n",
       "\n",
       "   reference alternate  \n",
       "0          C         T  \n",
       "5          C         T  \n",
       "11         T         C  \n",
       "0          C         T  \n",
       "5       None      None  \n",
       "..       ...       ...  \n",
       "2       None      None  \n",
       "7          C         T  \n",
       "11         A         G  \n",
       "16         C         T  \n",
       "18         G         T  \n",
       "\n",
       "[132 rows x 8 columns]"
      ]
     },
     "execution_count": 246,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[lineages.protein.isin([\"del\", \"nuc\"])]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 247,
   "id": "7391900c-b70d-41f6-aadd-162f115923a9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['nsp3', 'nsp6', 'S', 'ORF8', 'N', 'nuc', 'nsp5', 'ORF7a', 'ORF1a',\n",
       "       'ORF1b', 'nsp4', 'del', 'nsp15', 'M', 'spike', 'ORF3a', '1ab',\n",
       "       'orf1a', 'orf1b', 'orf3a', 'n', 'nsp13', 's', '8', 'nsp12', 'E',\n",
       "       'ORF1ab', 'NSP2', 'orf1ab', 'e', 'm', 'nsp7', 'orf6'], dtype=object)"
      ]
     },
     "execution_count": 247,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages.protein.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 248,
   "id": "02be15c4-d02e-4f7e-bca2-06b9b9e98f09",
   "metadata": {},
   "outputs": [],
   "source": [
    "def annotate_position(position):\n",
    "    if position is None or position == np.nan:\n",
    "        return None\n",
    "    result = gene_coordinates[(gene_coordinates.start <= position) & (gene_coordinates.end > position)].gene_name\n",
    "    if result.shape[0] == 0:\n",
    "        return None\n",
    "    return result.iloc[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 260,
   "id": "cd982be8-93b5-445e-af84-2f69bb93c39c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['ORF1ab', 'S', 'ORF8', 'N', 'ORF6', 'ORF7a', 'M', None, 'ORF3a',\n",
       "       'E', 'ORF7b'], dtype=object)"
      ]
     },
     "execution_count": 260,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "protein_synonyms = {\n",
    "    \"S\": [\"S\", \"s\", \"spike\"],\n",
    "    \"N\": [\"N\", \"n\"],\n",
    "    \"M\": [\"M\", \"m\"],\n",
    "    \"E\": [\"E\", \"e\"],\n",
    "    \"ORF1ab\": [\"ORF1ab\", \"1ab\", \"orf1ab\", \"ORF1a\", \"ORF1b\", \"orf1a\", \"orf1b\", \"nsp3\", \"nsp6\", \"nsp5\", \"nsp4\", \"nsp15\", \"nsp13\", \"nsp7\", \"nsp12\", \"NSP2\"],\n",
    "    \"ORF3a\": [\"ORF3a\", \"orf3a\"],\n",
    "    \"ORF8\": [\"ORF8\", \"8\"],\n",
    "    \"ORF6\": [\"ORF6\", \"orf6\"]\n",
    "}\n",
    "\n",
    "\n",
    "def normalize_protein(protein):\n",
    "    for canonical_name, synonyms in protein_synonyms.items():\n",
    "        if protein in synonyms:\n",
    "            return canonical_name\n",
    "    return protein\n",
    "\n",
    "lineages[\"protein_normalized\"] = lineages[[\"protein\", \"position\"]].apply(lambda x: normalize_protein(x[0]) if x[0] != \"nuc\" and x[0] != \"del\" else annotate_position(x[1]), axis=1)\n",
    "\n",
    "lineages.reference.fillna(\"\", inplace=True)\n",
    "lineages.alternate.fillna(\"\", inplace=True)\n",
    "\n",
    "lineages[\"protein_normalized\"].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 261,
   "id": "cb224361-d039-40e4-b746-927c2b4ebebf",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "      <th>protein_normalized</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>del:11287:9</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>11287</td>\n",
       "      <td>11287.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>del:21990:3</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>21990</td>\n",
       "      <td>21990.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>del:27887:15</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>27887</td>\n",
       "      <td>27887.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>del:28895:3</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>28895</td>\n",
       "      <td>28895.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>del:22280:9</td>\n",
       "      <td>B.1.351</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>22280</td>\n",
       "      <td>22280.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>del:11287:9</td>\n",
       "      <td>B.1.351</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>11287</td>\n",
       "      <td>11287.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>del:28362:9</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>28362</td>\n",
       "      <td>28362.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>del:11287:9</td>\n",
       "      <td>P.1</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>11287</td>\n",
       "      <td>11287.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>del:21980:9</td>\n",
       "      <td>P.3</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>21980</td>\n",
       "      <td>21980.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>del:6513:3</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>6513</td>\n",
       "      <td>6513.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>del:21765:6</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21765</td>\n",
       "      <td>21765.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>del:21987:9</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21987</td>\n",
       "      <td>21987.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>del:22194:3</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>22194</td>\n",
       "      <td>22194.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>del:28362:9</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>28362</td>\n",
       "      <td>28362.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>del:21765:6</td>\n",
       "      <td>BA.3</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21765</td>\n",
       "      <td>21765.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>del:21987:9</td>\n",
       "      <td>BA.3</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21987</td>\n",
       "      <td>21987.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>del:22194:3</td>\n",
       "      <td>BA.3</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>22194</td>\n",
       "      <td>22194.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>del:28362:9</td>\n",
       "      <td>BA.3</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>28362</td>\n",
       "      <td>28362.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>del:21633:9</td>\n",
       "      <td>BA.2</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21633</td>\n",
       "      <td>21633.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>del:28362:9</td>\n",
       "      <td>BA.2</td>\n",
       "      <td>None</td>\n",
       "      <td>del</td>\n",
       "      <td>28362</td>\n",
       "      <td>28362.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>N</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>del:28271:1</td>\n",
       "      <td>AY.4</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>28271</td>\n",
       "      <td>28271.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>del:22029:6</td>\n",
       "      <td>AY.4</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>22029</td>\n",
       "      <td>22029.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>del:28248:6</td>\n",
       "      <td>AY.4</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>28248</td>\n",
       "      <td>28248.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>del:28271:1</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>28271</td>\n",
       "      <td>28271.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>del:22029:6</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>22029</td>\n",
       "      <td>22029.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>del:28248:6</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>del</td>\n",
       "      <td>28248</td>\n",
       "      <td>28248.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>ORF8</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           sites    lineage parent_lineage protein mutation  position  \\\n",
       "5    del:11287:9  B.1.1.318           None     del    11287   11287.0   \n",
       "8    del:21990:3  B.1.1.318           None     del    21990   21990.0   \n",
       "15  del:27887:15  B.1.1.318           None     del    27887   27887.0   \n",
       "18   del:28895:3  B.1.1.318           None     del    28895   28895.0   \n",
       "12   del:22280:9    B.1.351           None     del    22280   22280.0   \n",
       "13   del:11287:9    B.1.351           None     del    11287   11287.0   \n",
       "34   del:28362:9  B.1.1.529           None     del    28362   28362.0   \n",
       "4    del:11287:9        P.1           None     del    11287   11287.0   \n",
       "5    del:21980:9        P.3           None     del    21980   21980.0   \n",
       "2     del:6513:3       BA.1      B.1.1.529     del     6513    6513.0   \n",
       "9    del:21765:6       BA.1      B.1.1.529     del    21765   21765.0   \n",
       "11   del:21987:9       BA.1      B.1.1.529     del    21987   21987.0   \n",
       "12   del:22194:3       BA.1      B.1.1.529     del    22194   22194.0   \n",
       "34   del:28362:9       BA.1           None     del    28362   28362.0   \n",
       "10   del:21765:6       BA.3      B.1.1.529     del    21765   21765.0   \n",
       "11   del:21987:9       BA.3      B.1.1.529     del    21987   21987.0   \n",
       "12   del:22194:3       BA.3      B.1.1.529     del    22194   22194.0   \n",
       "34   del:28362:9       BA.3           None     del    28362   28362.0   \n",
       "17   del:21633:9       BA.2      B.1.1.529     del    21633   21633.0   \n",
       "34   del:28362:9       BA.2           None     del    28362   28362.0   \n",
       "0    del:28271:1       AY.4      B.1.617.2     del    28271   28271.0   \n",
       "1    del:22029:6       AY.4      B.1.617.2     del    22029   22029.0   \n",
       "2    del:28248:6       AY.4      B.1.617.2     del    28248   28248.0   \n",
       "0    del:28271:1     AY.4.2      B.1.617.2     del    28271   28271.0   \n",
       "1    del:22029:6     AY.4.2      B.1.617.2     del    22029   22029.0   \n",
       "2    del:28248:6     AY.4.2      B.1.617.2     del    28248   28248.0   \n",
       "\n",
       "   reference alternate protein_normalized  \n",
       "5                                  ORF1ab  \n",
       "8                                       S  \n",
       "15                                   None  \n",
       "18                                      N  \n",
       "12                                      S  \n",
       "13                                 ORF1ab  \n",
       "34                                      N  \n",
       "4                                  ORF1ab  \n",
       "5                                       S  \n",
       "2                                  ORF1ab  \n",
       "9                                       S  \n",
       "11                                      S  \n",
       "12                                      S  \n",
       "34                                      N  \n",
       "10                                      S  \n",
       "11                                      S  \n",
       "12                                      S  \n",
       "34                                      N  \n",
       "17                                      S  \n",
       "34                                      N  \n",
       "0                                    None  \n",
       "1                                       S  \n",
       "2                                    ORF8  \n",
       "0                                    None  \n",
       "1                                       S  \n",
       "2                                    ORF8  "
      ]
     },
     "execution_count": 261,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[lineages.protein == \"del\"].head(50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 219,
   "id": "2b5f85d3-6d56-4e10-bcb2-afd36bbdf468",
   "metadata": {},
   "outputs": [
    {
     "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>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "      <th>protein_normalized</th>\n",
       "      <th>annotated_protein</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nuc:C835T</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C835T</td>\n",
       "      <td>835</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>nuc:C16293T</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C16293T</td>\n",
       "      <td>16293</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>nuc:T27384C</td>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>T27384C</td>\n",
       "      <td>27384</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nuc:C3961T</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C3961T</td>\n",
       "      <td>3961</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>nuc:T23287C</td>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>None</td>\n",
       "      <td>nuc</td>\n",
       "      <td>T23287C</td>\n",
       "      <td>23287</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>nuc</td>\n",
       "      <td>S</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>nuc:T17040C</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>AY.4</td>\n",
       "      <td>nuc</td>\n",
       "      <td>T17040C</td>\n",
       "      <td>17040</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>nuc:C8986T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C8986T</td>\n",
       "      <td>8986</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>nuc:A11332G</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>A11332G</td>\n",
       "      <td>11332</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF1ab</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>nuc:C27874T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C27874T</td>\n",
       "      <td>27874</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>ORF7b</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>nuc:G29742T</td>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>nuc</td>\n",
       "      <td>G29742T</td>\n",
       "      <td>29742</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>nuc</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>106 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          sites    lineage parent_lineage protein mutation position reference  \\\n",
       "0     nuc:C835T  B.1.617.3           None     nuc    C835T      835         C   \n",
       "5   nuc:C16293T  B.1.617.3           None     nuc  C16293T    16293         C   \n",
       "11  nuc:T27384C  B.1.617.3           None     nuc  T27384C    27384         T   \n",
       "0    nuc:C3961T  B.1.1.318           None     nuc   C3961T     3961         C   \n",
       "10  nuc:T23287C  B.1.1.318           None     nuc  T23287C    23287         T   \n",
       "..          ...        ...            ...     ...      ...      ...       ...   \n",
       "0   nuc:T17040C     AY.4.2           AY.4     nuc  T17040C    17040         T   \n",
       "7    nuc:C8986T     AY.4.2      B.1.617.2     nuc   C8986T     8986         C   \n",
       "11  nuc:A11332G     AY.4.2      B.1.617.2     nuc  A11332G    11332         A   \n",
       "16  nuc:C27874T     AY.4.2      B.1.617.2     nuc  C27874T    27874         C   \n",
       "18  nuc:G29742T     AY.4.2      B.1.617.2     nuc  G29742T    29742         G   \n",
       "\n",
       "   alternate protein_normalized annotated_protein  \n",
       "0          T                nuc            ORF1ab  \n",
       "5          T                nuc            ORF1ab  \n",
       "11         C                nuc              ORF6  \n",
       "0          T                nuc            ORF1ab  \n",
       "10         C                nuc                 S  \n",
       "..       ...                ...               ...  \n",
       "0          C                nuc            ORF1ab  \n",
       "7          T                nuc            ORF1ab  \n",
       "11         G                nuc            ORF1ab  \n",
       "16         T                nuc             ORF7b  \n",
       "18         T                nuc              None  \n",
       "\n",
       "[106 rows x 10 columns]"
      ]
     },
     "execution_count": 219,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[lineages.protein == \"nuc\"][\"protein_normalized\"] = lineages[lineages.protein == \"nuc\"].position.transform(annotate_position)\n",
    "lineages[lineages.protein == \"nuc\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 256,
   "id": "098ec2d8-31a6-4588-8853-fb6bcaa6ecad",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "A.23.1    ORF1ab                     4\n",
      "AY.4      ORF1ab                    13\n",
      "AY.4.2    ORF1ab                    14\n",
      "B.1.1.318 ORF1ab                     7\n",
      "B.1.1.529 ORF1ab                     6\n",
      "B.1.1.7   ORF1ab                     9\n",
      "B.1.351   ORF1ab                     4\n",
      "B.1.427   ORF1ab                     4\n",
      "B.1.429   ORF1ab                     4\n",
      "B.1.525   ORF1ab                     7\n",
      "B.1.526   ORF1ab                     7\n",
      "B.1.617.1 ORF1ab                     5\n",
      "B.1.617.3 ORF1ab                     6\n",
      "B.1.621   ORF1ab                    12\n",
      "BA.1      ORF1ab                    14\n",
      "BA.2      ORF1ab                    22\n",
      "BA.3      ORF1ab                    15\n",
      "C.37      ORF1ab                     8\n",
      "P.1       ORF1ab                     7\n",
      "P.2       ORF1ab                     3\n",
      "P.3       ORF1ab                     7\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "A.23.1    S                          6\n",
      "AV.1      S                         10\n",
      "AY.4      S                          7\n",
      "AY.4.2    S                          9\n",
      "B.1.1.318 S                          7\n",
      "B.1.1.529 S                         21\n",
      "B.1.1.7   S                          9\n",
      "B.1.351   S                          6\n",
      "B.1.427   S                          4\n",
      "B.1.429   S                          5\n",
      "B.1.525   S                          5\n",
      "B.1.526   S                          8\n",
      "B.1.617.1 S                          3\n",
      "B.1.617.2 S                          6\n",
      "B.1.617.3 S                          5\n",
      "B.1.621   S                          8\n",
      "BA.1      S                         33\n",
      "BA.2      S                         29\n",
      "BA.3      S                         28\n",
      "C.37      S                          7\n",
      "P.1       S                          6\n",
      "P.2       S                          1\n",
      "P.3       S                          9\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "A.23.1    ORF8                       2\n",
      "AY.4      ORF8                       1\n",
      "AY.4.2    ORF8                       1\n",
      "B.1.1.318 ORF8                       1\n",
      "B.1.1.7   ORF8                       3\n",
      "B.1.526   ORF8                       1\n",
      "B.1.617.3 ORF8                       1\n",
      "B.1.621   ORF8                       3\n",
      "P.1       ORF8                       1\n",
      "P.2       ORF8                       1\n",
      "P.3       ORF8                       1\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "A.23.1    N                          1\n",
      "AV.1      N                          3\n",
      "AY.4      N                          4\n",
      "AY.4.2    N                          4\n",
      "B.1.1.318 N                          1\n",
      "B.1.1.529 N                          3\n",
      "B.1.1.7   N                          2\n",
      "B.1.351   N                          1\n",
      "B.1.427   N                          1\n",
      "B.1.429   N                          1\n",
      "B.1.525   N                          1\n",
      "B.1.526   N                          4\n",
      "B.1.617.1 N                          1\n",
      "B.1.617.2 N                          3\n",
      "B.1.617.3 N                          3\n",
      "B.1.621   N                          1\n",
      "BA.1      N                          3\n",
      "BA.2      N                          4\n",
      "BA.3      N                          4\n",
      "C.37      N                          4\n",
      "P.1       N                          1\n",
      "P.2       N                          2\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "B.1.1.529 ORF6                       1\n",
      "B.1.617.3 ORF6                       1\n",
      "BA.1      ORF6                       1\n",
      "BA.2      ORF6                       2\n",
      "BA.3      ORF6                       1\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "AY.4      ORF7a                      2\n",
      "AY.4.2    ORF7a                      2\n",
      "B.1.617.1 ORF7a                      1\n",
      "B.1.617.2 ORF7a                      2\n",
      "B.1.617.3 ORF7a                      1\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "AV.1      M                          2\n",
      "AY.4      M                          1\n",
      "AY.4.2    M                          1\n",
      "B.1.1.318 M                          1\n",
      "B.1.1.529 M                          2\n",
      "B.1.1.7   M                          1\n",
      "B.1.427   M                          1\n",
      "B.1.429   M                          1\n",
      "B.1.525   M                          1\n",
      "B.1.617.2 M                          1\n",
      "BA.1      M                          3\n",
      "BA.2      M                          3\n",
      "BA.3      M                          3\n",
      "Empty DataFrame\n",
      "Columns: [mutation]\n",
      "Index: []\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "AY.4      ORF3a                      1\n",
      "AY.4.2    ORF3a                      1\n",
      "B.1.351   ORF3a                      2\n",
      "B.1.427   ORF3a                      1\n",
      "B.1.429   ORF3a                      1\n",
      "B.1.526   ORF3a                      2\n",
      "B.1.617.1 ORF3a                      1\n",
      "B.1.617.2 ORF3a                      1\n",
      "B.1.621   ORF3a                      1\n",
      "BA.1      ORF3a                      1\n",
      "BA.2      ORF3a                      2\n",
      "BA.3      ORF3a                      1\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "B.1.1.529 E                          1\n",
      "B.1.351   E                          1\n",
      "B.1.525   E                          1\n",
      "BA.1      E                          1\n",
      "BA.2      E                          1\n",
      "BA.3      E                          1\n",
      "                              mutation\n",
      "lineage   protein_normalized          \n",
      "AY.4      ORF7b                      1\n",
      "AY.4.2    ORF7b                      1\n",
      "B.1.1.529 ORF7b                      1\n",
      "BA.1      ORF7b                      1\n",
      "BA.2      ORF7b                      1\n",
      "BA.3      ORF7b                      1\n"
     ]
    }
   ],
   "source": [
    "for p in lineages.protein_normalized.unique():\n",
    "    print(lineages[lineages.protein_normalized == p][[\"lineage\", \"protein_normalized\", \"mutation\"]].groupby([\"lineage\", \"protein_normalized\"]).count())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 257,
   "id": "7dc215e4-cd9e-4647-b4b5-94b33aea83b4",
   "metadata": {},
   "outputs": [
    {
     "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>mutation</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>protein_normalized</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>E</th>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>M</th>\n",
       "      <td>21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N</th>\n",
       "      <td>52</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF1ab</th>\n",
       "      <td>178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF3a</th>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF6</th>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF7a</th>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF7b</th>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ORF8</th>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>232</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    mutation\n",
       "protein_normalized          \n",
       "E                          6\n",
       "M                         21\n",
       "N                         52\n",
       "ORF1ab                   178\n",
       "ORF3a                     15\n",
       "ORF6                       6\n",
       "ORF7a                      8\n",
       "ORF7b                      6\n",
       "ORF8                      16\n",
       "S                        232"
      ]
     },
     "execution_count": 257,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[[\"protein_normalized\", \"mutation\"]].groupby(\"protein_normalized\").count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6c057c87-e3cb-46d2-88a1-a54293d4ef77",
   "metadata": {},
   "outputs": [],
   "source": [
    "lineages"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "38746a32-276e-4fc7-977e-ca0f09604d0a",
   "metadata": {},
   "source": [
    "## Aromatic and other large AAs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 258,
   "id": "b74bb156-63f2-4763-8fab-a8efc5cc4278",
   "metadata": {},
   "outputs": [],
   "source": [
    "aromatic_aas = [\"F\", \"W\", \"Y\", \"H\"]\n",
    "large_aas = [\"I\", \"L\", \"M\", \"K\", \"R\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 262,
   "id": "b570286e-53a9-479a-88a2-95f5ce91f86d",
   "metadata": {},
   "outputs": [],
   "source": [
    "lineages[\"removal_aromatic\"] = lineages[[\"reference\", \"alternate\"]].apply(lambda r: any([aa in r[0] for aa in aromatic_aas]) and all([not aa in r[1] for aa in aromatic_aas]), axis=1)\n",
    "lineages[\"removal_large\"] = lineages[[\"reference\", \"alternate\"]].apply(lambda r: any([aa in r[0] for aa in large_aas]) and all([not aa in r[1] for aa in large_aas]), axis=1)\n",
    "lineages[\"add_aromatic\"] = lineages[[\"reference\", \"alternate\"]].apply(lambda r: any([aa in r[1] for aa in aromatic_aas]) and all([not aa in r[0] for aa in aromatic_aas]), axis=1)\n",
    "lineages[\"add_large\"] = lineages[[\"reference\", \"alternate\"]].apply(lambda r: any([aa in r[1] for aa in large_aas]) and all([not aa in r[0] for aa in large_aas]), axis=1)\n",
    "lineages[\"count\"] = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 263,
   "id": "d847de14-df00-4deb-85b5-41c3a66a3b6c",
   "metadata": {},
   "outputs": [
    {
     "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>lineage</th>\n",
       "      <th>count</th>\n",
       "      <th>removal_aromatic</th>\n",
       "      <th>add_aromatic</th>\n",
       "      <th>removal_large</th>\n",
       "      <th>add_large</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A.23.1</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AV.1</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AY.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>21</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>B.1.1.7</td>\n",
       "      <td>9</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>B.1.351</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>B.1.427</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>B.1.429</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>B.1.525</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>B.1.526</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>B.1.617.1</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>B.1.621</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>BA.1</td>\n",
       "      <td>33</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>BA.2</td>\n",
       "      <td>29</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>BA.3</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>C.37</td>\n",
       "      <td>7</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>P.1</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>P.2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>P.3</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      lineage  count  removal_aromatic  add_aromatic  removal_large  add_large\n",
       "0      A.23.1      6                 1             2              0          3\n",
       "1        AV.1     10                 1             2              1          3\n",
       "2        AY.4      7                 0             0              0          3\n",
       "3      AY.4.2      9                 0             0              0          3\n",
       "4   B.1.1.318      7                 0             2              0          2\n",
       "5   B.1.1.529     21                 0             5              1          7\n",
       "6     B.1.1.7      9                 2             3              0          2\n",
       "7     B.1.351      6                 0             1              0          1\n",
       "8     B.1.427      4                 1             0              0          1\n",
       "9     B.1.429      5                 1             0              0          1\n",
       "10    B.1.525      5                 1             1              0          3\n",
       "11    B.1.526      8                 0             1              1          3\n",
       "12  B.1.617.1      3                 0             0              0          1\n",
       "13  B.1.617.2      6                 0             0              0          3\n",
       "14  B.1.617.3      5                 0             0              0          2\n",
       "15    B.1.621      8                 1             2              0          2\n",
       "16       BA.1     33                 0             6              2         11\n",
       "17       BA.2     29                 0             6              2          8\n",
       "18       BA.3     28                 0             6              1          7\n",
       "19       C.37      7                 2             0              2          1\n",
       "20        P.1      6                 0             1              1          2\n",
       "21        P.2      1                 0             0              0          1\n",
       "22        P.3      9                 0             3              0          2"
      ]
     },
     "execution_count": 263,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages_mutation_types = lineages[(lineages.protein_normalized == \"S\")][[\"lineage\", \"count\", \"removal_aromatic\", \"add_aromatic\", \"removal_large\", \"add_large\"]].groupby(\"lineage\").sum().reset_index()\n",
    "lineages_mutation_types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 264,
   "id": "52f1e4c0-df42-421e-b4c9-6d2ab9e4044f",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>lineage</th>\n",
       "      <th>count</th>\n",
       "      <th>removal_aromatic</th>\n",
       "      <th>add_aromatic</th>\n",
       "      <th>removal_large</th>\n",
       "      <th>add_large</th>\n",
       "      <th>ratio_removal_aromatic</th>\n",
       "      <th>ratio_removal_large</th>\n",
       "      <th>ratio_add_aromatic</th>\n",
       "      <th>ratio_add_large</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A.23.1</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0.500000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AV.1</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>0.200000</td>\n",
       "      <td>0.300000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AY.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.428571</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.333333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.285714</td>\n",
       "      <td>0.285714</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>21</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.047619</td>\n",
       "      <td>0.238095</td>\n",
       "      <td>0.333333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>B.1.1.7</td>\n",
       "      <td>9</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0.222222</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0.222222</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>B.1.351</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.166667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>B.1.427</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0.250000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.250000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>B.1.429</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0.200000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.200000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>B.1.525</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.200000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.200000</td>\n",
       "      <td>0.600000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>B.1.526</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.125000</td>\n",
       "      <td>0.125000</td>\n",
       "      <td>0.375000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>B.1.617.1</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.333333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>B.1.617.2</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.500000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>B.1.617.3</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.400000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>B.1.621</td>\n",
       "      <td>8</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0.125000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.250000</td>\n",
       "      <td>0.250000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>BA.1</td>\n",
       "      <td>33</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>11</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.060606</td>\n",
       "      <td>0.181818</td>\n",
       "      <td>0.333333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>BA.2</td>\n",
       "      <td>29</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.068966</td>\n",
       "      <td>0.206897</td>\n",
       "      <td>0.275862</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>BA.3</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.035714</td>\n",
       "      <td>0.214286</td>\n",
       "      <td>0.250000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>C.37</td>\n",
       "      <td>7</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0.285714</td>\n",
       "      <td>0.285714</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.142857</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>P.1</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.166667</td>\n",
       "      <td>0.333333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>P.2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>P.3</td>\n",
       "      <td>9</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0.222222</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      lineage  count  removal_aromatic  add_aromatic  removal_large  \\\n",
       "0      A.23.1      6                 1             2              0   \n",
       "1        AV.1     10                 1             2              1   \n",
       "2        AY.4      7                 0             0              0   \n",
       "3      AY.4.2      9                 0             0              0   \n",
       "4   B.1.1.318      7                 0             2              0   \n",
       "5   B.1.1.529     21                 0             5              1   \n",
       "6     B.1.1.7      9                 2             3              0   \n",
       "7     B.1.351      6                 0             1              0   \n",
       "8     B.1.427      4                 1             0              0   \n",
       "9     B.1.429      5                 1             0              0   \n",
       "10    B.1.525      5                 1             1              0   \n",
       "11    B.1.526      8                 0             1              1   \n",
       "12  B.1.617.1      3                 0             0              0   \n",
       "13  B.1.617.2      6                 0             0              0   \n",
       "14  B.1.617.3      5                 0             0              0   \n",
       "15    B.1.621      8                 1             2              0   \n",
       "16       BA.1     33                 0             6              2   \n",
       "17       BA.2     29                 0             6              2   \n",
       "18       BA.3     28                 0             6              1   \n",
       "19       C.37      7                 2             0              2   \n",
       "20        P.1      6                 0             1              1   \n",
       "21        P.2      1                 0             0              0   \n",
       "22        P.3      9                 0             3              0   \n",
       "\n",
       "    add_large  ratio_removal_aromatic  ratio_removal_large  \\\n",
       "0           3                0.166667             0.000000   \n",
       "1           3                0.100000             0.100000   \n",
       "2           3                0.000000             0.000000   \n",
       "3           3                0.000000             0.000000   \n",
       "4           2                0.000000             0.000000   \n",
       "5           7                0.000000             0.047619   \n",
       "6           2                0.222222             0.000000   \n",
       "7           1                0.000000             0.000000   \n",
       "8           1                0.250000             0.000000   \n",
       "9           1                0.200000             0.000000   \n",
       "10          3                0.200000             0.000000   \n",
       "11          3                0.000000             0.125000   \n",
       "12          1                0.000000             0.000000   \n",
       "13          3                0.000000             0.000000   \n",
       "14          2                0.000000             0.000000   \n",
       "15          2                0.125000             0.000000   \n",
       "16         11                0.000000             0.060606   \n",
       "17          8                0.000000             0.068966   \n",
       "18          7                0.000000             0.035714   \n",
       "19          1                0.285714             0.285714   \n",
       "20          2                0.000000             0.166667   \n",
       "21          1                0.000000             0.000000   \n",
       "22          2                0.000000             0.000000   \n",
       "\n",
       "    ratio_add_aromatic  ratio_add_large  \n",
       "0             0.333333         0.500000  \n",
       "1             0.200000         0.300000  \n",
       "2             0.000000         0.428571  \n",
       "3             0.000000         0.333333  \n",
       "4             0.285714         0.285714  \n",
       "5             0.238095         0.333333  \n",
       "6             0.333333         0.222222  \n",
       "7             0.166667         0.166667  \n",
       "8             0.000000         0.250000  \n",
       "9             0.000000         0.200000  \n",
       "10            0.200000         0.600000  \n",
       "11            0.125000         0.375000  \n",
       "12            0.000000         0.333333  \n",
       "13            0.000000         0.500000  \n",
       "14            0.000000         0.400000  \n",
       "15            0.250000         0.250000  \n",
       "16            0.181818         0.333333  \n",
       "17            0.206897         0.275862  \n",
       "18            0.214286         0.250000  \n",
       "19            0.000000         0.142857  \n",
       "20            0.166667         0.333333  \n",
       "21            0.000000         1.000000  \n",
       "22            0.333333         0.222222  "
      ]
     },
     "execution_count": 264,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages_mutation_types[\"ratio_removal_aromatic\"] = lineages_mutation_types[\"removal_aromatic\"] / lineages_mutation_types[\"count\"]\n",
    "lineages_mutation_types[\"ratio_removal_large\"] = lineages_mutation_types[\"removal_large\"] / lineages_mutation_types[\"count\"]\n",
    "lineages_mutation_types[\"ratio_add_aromatic\"] = lineages_mutation_types[\"add_aromatic\"] / lineages_mutation_types[\"count\"]\n",
    "lineages_mutation_types[\"ratio_add_large\"] = lineages_mutation_types[\"add_large\"] / lineages_mutation_types[\"count\"]\n",
    "lineages_mutation_types"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 145,
   "id": "9938e21b-e741-4c04-ae99-b5511542b36f",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
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       "      <th>removal_aromatic</th>\n",
       "      <th>removal_large</th>\n",
       "      <th>add_aromatic</th>\n",
       "      <th>add_large</th>\n",
       "      <th>count</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>spike:G142D</td>\n",
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       "      <td>spike</td>\n",
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       "      <td>G</td>\n",
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       "      <th>7</th>\n",
       "      <td>spike:G339D</td>\n",
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       "      <td>spike</td>\n",
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       "      <td>G</td>\n",
       "      <td>D</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>spike:S373P</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S373P</td>\n",
       "      <td>373</td>\n",
       "      <td>S</td>\n",
       "      <td>P</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>spike:S375F</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S375F</td>\n",
       "      <td>375</td>\n",
       "      <td>S</td>\n",
       "      <td>F</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>spike:K417N</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>K417N</td>\n",
       "      <td>417</td>\n",
       "      <td>K</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>spike:N440K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N440K</td>\n",
       "      <td>440</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>spike:S477N</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S477N</td>\n",
       "      <td>477</td>\n",
       "      <td>S</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>spike:T478K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>T478K</td>\n",
       "      <td>478</td>\n",
       "      <td>T</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>spike:E484A</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>E484A</td>\n",
       "      <td>484</td>\n",
       "      <td>E</td>\n",
       "      <td>A</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>spike:Q493R</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q493R</td>\n",
       "      <td>493</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>spike:Q498R</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q498R</td>\n",
       "      <td>498</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>spike:N501Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N501Y</td>\n",
       "      <td>501</td>\n",
       "      <td>N</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>spike:Y505H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Y505H</td>\n",
       "      <td>505</td>\n",
       "      <td>Y</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>spike:D614G</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D614G</td>\n",
       "      <td>614</td>\n",
       "      <td>D</td>\n",
       "      <td>G</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>spike:H655Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>H655Y</td>\n",
       "      <td>655</td>\n",
       "      <td>H</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>spike:N679K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N679K</td>\n",
       "      <td>679</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>spike:P681H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>P681H</td>\n",
       "      <td>681</td>\n",
       "      <td>P</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>spike:N764K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N764K</td>\n",
       "      <td>764</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>spike:D796Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D796Y</td>\n",
       "      <td>796</td>\n",
       "      <td>D</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>spike:Q954H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q954H</td>\n",
       "      <td>954</td>\n",
       "      <td>Q</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>spike:N969K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N969K</td>\n",
       "      <td>969</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          sites    lineage parent_lineage protein mutation position reference  \\\n",
       "6   spike:G142D  B.1.1.529           None   spike    G142D      142         G   \n",
       "7   spike:G339D  B.1.1.529           None   spike    G339D      339         G   \n",
       "8   spike:S373P  B.1.1.529           None   spike    S373P      373         S   \n",
       "9   spike:S375F  B.1.1.529           None   spike    S375F      375         S   \n",
       "10  spike:K417N  B.1.1.529           None   spike    K417N      417         K   \n",
       "11  spike:N440K  B.1.1.529           None   spike    N440K      440         N   \n",
       "12  spike:S477N  B.1.1.529           None   spike    S477N      477         S   \n",
       "13  spike:T478K  B.1.1.529           None   spike    T478K      478         T   \n",
       "14  spike:E484A  B.1.1.529           None   spike    E484A      484         E   \n",
       "15  spike:Q493R  B.1.1.529           None   spike    Q493R      493         Q   \n",
       "16  spike:Q498R  B.1.1.529           None   spike    Q498R      498         Q   \n",
       "17  spike:N501Y  B.1.1.529           None   spike    N501Y      501         N   \n",
       "18  spike:Y505H  B.1.1.529           None   spike    Y505H      505         Y   \n",
       "19  spike:D614G  B.1.1.529           None   spike    D614G      614         D   \n",
       "20  spike:H655Y  B.1.1.529           None   spike    H655Y      655         H   \n",
       "21  spike:N679K  B.1.1.529           None   spike    N679K      679         N   \n",
       "22  spike:P681H  B.1.1.529           None   spike    P681H      681         P   \n",
       "23  spike:N764K  B.1.1.529           None   spike    N764K      764         N   \n",
       "24  spike:D796Y  B.1.1.529           None   spike    D796Y      796         D   \n",
       "25  spike:Q954H  B.1.1.529           None   spike    Q954H      954         Q   \n",
       "26  spike:N969K  B.1.1.529           None   spike    N969K      969         N   \n",
       "\n",
       "   alternate protein_normalized  removal_aromatic  removal_large  \\\n",
       "6          D                  S             False          False   \n",
       "7          D                  S             False          False   \n",
       "8          P                  S             False          False   \n",
       "9          F                  S             False          False   \n",
       "10         N                  S             False           True   \n",
       "11         K                  S             False          False   \n",
       "12         N                  S             False          False   \n",
       "13         K                  S             False          False   \n",
       "14         A                  S             False          False   \n",
       "15         R                  S             False          False   \n",
       "16         R                  S             False          False   \n",
       "17         Y                  S             False          False   \n",
       "18         H                  S             False          False   \n",
       "19         G                  S             False          False   \n",
       "20         Y                  S             False          False   \n",
       "21         K                  S             False          False   \n",
       "22         H                  S             False          False   \n",
       "23         K                  S             False          False   \n",
       "24         Y                  S             False          False   \n",
       "25         H                  S             False          False   \n",
       "26         K                  S             False          False   \n",
       "\n",
       "    add_aromatic  add_large  count  \n",
       "6          False      False   True  \n",
       "7          False      False   True  \n",
       "8          False      False   True  \n",
       "9           True      False   True  \n",
       "10         False      False   True  \n",
       "11         False       True   True  \n",
       "12         False      False   True  \n",
       "13         False       True   True  \n",
       "14         False      False   True  \n",
       "15         False       True   True  \n",
       "16         False       True   True  \n",
       "17          True      False   True  \n",
       "18         False      False   True  \n",
       "19         False      False   True  \n",
       "20         False      False   True  \n",
       "21         False       True   True  \n",
       "22          True      False   True  \n",
       "23         False       True   True  \n",
       "24          True      False   True  \n",
       "25          True      False   True  \n",
       "26         False       True   True  "
      ]
     },
     "execution_count": 145,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[(lineages.protein_normalized == \"S\") & (lineages.lineage == \"B.1.1.529\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 149,
   "id": "81e85c1f-fe01-4ea6-9b65-a6c10cc41491",
   "metadata": {},
   "outputs": [
    {
     "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>lineage</th>\n",
       "      <th>variable</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>A.23.1</td>\n",
       "      <td>count</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AV.1</td>\n",
       "      <td>count</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AY.4</td>\n",
       "      <td>count</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AY.4.2</td>\n",
       "      <td>count</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B.1.1.318</td>\n",
       "      <td>count</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>BA.3</td>\n",
       "      <td>add_large</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>111</th>\n",
       "      <td>C.37</td>\n",
       "      <td>add_large</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>112</th>\n",
       "      <td>P.1</td>\n",
       "      <td>add_large</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>P.2</td>\n",
       "      <td>add_large</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>P.3</td>\n",
       "      <td>add_large</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>115 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       lineage   variable  value\n",
       "0       A.23.1      count      6\n",
       "1         AV.1      count     10\n",
       "2         AY.4      count      6\n",
       "3       AY.4.2      count      8\n",
       "4    B.1.1.318      count      4\n",
       "..         ...        ...    ...\n",
       "110       BA.3  add_large      7\n",
       "111       C.37  add_large      1\n",
       "112        P.1  add_large      2\n",
       "113        P.2  add_large      1\n",
       "114        P.3  add_large      2\n",
       "\n",
       "[115 rows x 3 columns]"
      ]
     },
     "execution_count": 149,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.melt(lineages_mutation_types, id_vars = \"lineage\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 270,
   "id": "529c0506-2463-4adb-bc1b-04b4ffddfb85",
   "metadata": {},
   "outputs": [],
   "source": [
    "def plot_histogram(data, figname):\n",
    "    fig = plt.figure(figsize=(30, 14))\n",
    "    sns.barplot(data=data, x=\"lineage\", y=\"value\", hue=\"variable\")\n",
    "    plt.xticks(rotation=45)\n",
    "    plt.xlabel(None)\n",
    "    plt.ylabel(None)\n",
    "    plt.legend(title=None)\n",
    "    sns.despine(bottom=True, left=True)\n",
    "    fig.savefig(os.path.join(figures_folder, figname), dpi=dpi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 273,
   "id": "cda0b4cc-6a07-466c-a943-a8701b662ee1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 2160x1008 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot_histogram(\n",
    "    data=pd.melt(lineages_mutation_types[[\"lineage\", \"count\", \"removal_aromatic\", \"add_aromatic\", \"removal_large\", \"add_large\"]], id_vars = \"lineage\"),\n",
    "    figname=\"figure_01_lineages_mutation_counts.png\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 274,
   "id": "12e6b91f-3d5f-4330-8728-93cbf47790ca",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 2160x1008 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot_histogram(\n",
    "    data=pd.melt(lineages_mutation_types[[\"lineage\", \"ratio_removal_aromatic\", \"ratio_removal_large\"]], id_vars = \"lineage\"),\n",
    "    figname=\"figure_01_lineages_mutation_ratios_removaĺs.png\"\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 275,
   "id": "b031f5dd-61a8-4da3-bfc4-f02ae8151a57",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 2160x1008 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot_histogram(\n",
    "    data=pd.melt(lineages_mutation_types[[\"lineage\", \"ratio_add_aromatic\", \"ratio_add_large\"]], id_vars = \"lineage\"),\n",
    "    figname=\"figure_01_lineages_mutation_ratios_removaĺs.png\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e06e5069-4d2b-4f89-ac58-505a37bef6b9",
   "metadata": {},
   "source": [
    "## Building spike sequences for all lineages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 277,
   "id": "7c5acf41-84bc-4e1f-b5ad-e50bbedb87c2",
   "metadata": {},
   "outputs": [
    {
     "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>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "      <th>protein_normalized</th>\n",
       "      <th>removal_aromatic</th>\n",
       "      <th>removal_large</th>\n",
       "      <th>add_aromatic</th>\n",
       "      <th>add_large</th>\n",
       "      <th>count</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>spike:G142D</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>G142D</td>\n",
       "      <td>142.0</td>\n",
       "      <td>G</td>\n",
       "      <td>D</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>spike:G339D</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>G339D</td>\n",
       "      <td>339.0</td>\n",
       "      <td>G</td>\n",
       "      <td>D</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>spike:S373P</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S373P</td>\n",
       "      <td>373.0</td>\n",
       "      <td>S</td>\n",
       "      <td>P</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>spike:S375F</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S375F</td>\n",
       "      <td>375.0</td>\n",
       "      <td>S</td>\n",
       "      <td>F</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>spike:K417N</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>K417N</td>\n",
       "      <td>417.0</td>\n",
       "      <td>K</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>spike:N440K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N440K</td>\n",
       "      <td>440.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>spike:S477N</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S477N</td>\n",
       "      <td>477.0</td>\n",
       "      <td>S</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>spike:T478K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>T478K</td>\n",
       "      <td>478.0</td>\n",
       "      <td>T</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>spike:E484A</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>E484A</td>\n",
       "      <td>484.0</td>\n",
       "      <td>E</td>\n",
       "      <td>A</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>spike:Q493R</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q493R</td>\n",
       "      <td>493.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>spike:Q498R</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q498R</td>\n",
       "      <td>498.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>spike:N501Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N501Y</td>\n",
       "      <td>501.0</td>\n",
       "      <td>N</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>spike:Y505H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Y505H</td>\n",
       "      <td>505.0</td>\n",
       "      <td>Y</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>spike:D614G</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D614G</td>\n",
       "      <td>614.0</td>\n",
       "      <td>D</td>\n",
       "      <td>G</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>spike:H655Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>H655Y</td>\n",
       "      <td>655.0</td>\n",
       "      <td>H</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>spike:N679K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N679K</td>\n",
       "      <td>679.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>spike:P681H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>P681H</td>\n",
       "      <td>681.0</td>\n",
       "      <td>P</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>spike:N764K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N764K</td>\n",
       "      <td>764.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>spike:D796Y</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D796Y</td>\n",
       "      <td>796.0</td>\n",
       "      <td>D</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>spike:Q954H</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q954H</td>\n",
       "      <td>954.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>spike:N969K</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N969K</td>\n",
       "      <td>969.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          sites    lineage parent_lineage protein mutation  position  \\\n",
       "6   spike:G142D  B.1.1.529           None   spike    G142D     142.0   \n",
       "7   spike:G339D  B.1.1.529           None   spike    G339D     339.0   \n",
       "8   spike:S373P  B.1.1.529           None   spike    S373P     373.0   \n",
       "9   spike:S375F  B.1.1.529           None   spike    S375F     375.0   \n",
       "10  spike:K417N  B.1.1.529           None   spike    K417N     417.0   \n",
       "11  spike:N440K  B.1.1.529           None   spike    N440K     440.0   \n",
       "12  spike:S477N  B.1.1.529           None   spike    S477N     477.0   \n",
       "13  spike:T478K  B.1.1.529           None   spike    T478K     478.0   \n",
       "14  spike:E484A  B.1.1.529           None   spike    E484A     484.0   \n",
       "15  spike:Q493R  B.1.1.529           None   spike    Q493R     493.0   \n",
       "16  spike:Q498R  B.1.1.529           None   spike    Q498R     498.0   \n",
       "17  spike:N501Y  B.1.1.529           None   spike    N501Y     501.0   \n",
       "18  spike:Y505H  B.1.1.529           None   spike    Y505H     505.0   \n",
       "19  spike:D614G  B.1.1.529           None   spike    D614G     614.0   \n",
       "20  spike:H655Y  B.1.1.529           None   spike    H655Y     655.0   \n",
       "21  spike:N679K  B.1.1.529           None   spike    N679K     679.0   \n",
       "22  spike:P681H  B.1.1.529           None   spike    P681H     681.0   \n",
       "23  spike:N764K  B.1.1.529           None   spike    N764K     764.0   \n",
       "24  spike:D796Y  B.1.1.529           None   spike    D796Y     796.0   \n",
       "25  spike:Q954H  B.1.1.529           None   spike    Q954H     954.0   \n",
       "26  spike:N969K  B.1.1.529           None   spike    N969K     969.0   \n",
       "\n",
       "   reference alternate protein_normalized  removal_aromatic  removal_large  \\\n",
       "6          G         D                  S             False          False   \n",
       "7          G         D                  S             False          False   \n",
       "8          S         P                  S             False          False   \n",
       "9          S         F                  S             False          False   \n",
       "10         K         N                  S             False           True   \n",
       "11         N         K                  S             False          False   \n",
       "12         S         N                  S             False          False   \n",
       "13         T         K                  S             False          False   \n",
       "14         E         A                  S             False          False   \n",
       "15         Q         R                  S             False          False   \n",
       "16         Q         R                  S             False          False   \n",
       "17         N         Y                  S             False          False   \n",
       "18         Y         H                  S             False          False   \n",
       "19         D         G                  S             False          False   \n",
       "20         H         Y                  S             False          False   \n",
       "21         N         K                  S             False          False   \n",
       "22         P         H                  S             False          False   \n",
       "23         N         K                  S             False          False   \n",
       "24         D         Y                  S             False          False   \n",
       "25         Q         H                  S             False          False   \n",
       "26         N         K                  S             False          False   \n",
       "\n",
       "    add_aromatic  add_large  count  \n",
       "6          False      False   True  \n",
       "7          False      False   True  \n",
       "8          False      False   True  \n",
       "9           True      False   True  \n",
       "10         False      False   True  \n",
       "11         False       True   True  \n",
       "12         False      False   True  \n",
       "13         False       True   True  \n",
       "14         False      False   True  \n",
       "15         False       True   True  \n",
       "16         False       True   True  \n",
       "17          True      False   True  \n",
       "18         False      False   True  \n",
       "19         False      False   True  \n",
       "20         False      False   True  \n",
       "21         False       True   True  \n",
       "22          True      False   True  \n",
       "23         False       True   True  \n",
       "24          True      False   True  \n",
       "25          True      False   True  \n",
       "26         False       True   True  "
      ]
     },
     "execution_count": 277,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[(lineages.lineage == \"B.1.1.529\") & (lineages.protein_normalized == \"S\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 278,
   "id": "e4128e67-92b0-4912-ab36-dc7c0d09ccd2",
   "metadata": {},
   "outputs": [
    {
     "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>sites</th>\n",
       "      <th>lineage</th>\n",
       "      <th>parent_lineage</th>\n",
       "      <th>protein</th>\n",
       "      <th>mutation</th>\n",
       "      <th>position</th>\n",
       "      <th>reference</th>\n",
       "      <th>alternate</th>\n",
       "      <th>protein_normalized</th>\n",
       "      <th>removal_aromatic</th>\n",
       "      <th>removal_large</th>\n",
       "      <th>add_aromatic</th>\n",
       "      <th>add_large</th>\n",
       "      <th>count</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>spike:A67V</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>A67V</td>\n",
       "      <td>67.0</td>\n",
       "      <td>A</td>\n",
       "      <td>V</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>del:21765:6</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21765</td>\n",
       "      <td>21765.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>spike:T95I</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>T95I</td>\n",
       "      <td>95.0</td>\n",
       "      <td>T</td>\n",
       "      <td>I</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>del:21987:9</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>21987</td>\n",
       "      <td>21987.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>del:22194:3</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>del</td>\n",
       "      <td>22194</td>\n",
       "      <td>22194.0</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>spike:S371L</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>S371L</td>\n",
       "      <td>371.0</td>\n",
       "      <td>S</td>\n",
       "      <td>L</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>spike:G446S</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>G446S</td>\n",
       "      <td>446.0</td>\n",
       "      <td>G</td>\n",
       "      <td>S</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>spike:G496S</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>G496S</td>\n",
       "      <td>496.0</td>\n",
       "      <td>G</td>\n",
       "      <td>S</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>spike:T547K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>T547K</td>\n",
       "      <td>547.0</td>\n",
       "      <td>T</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>spike:N856K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>N856K</td>\n",
       "      <td>856.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>spike:L981F</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>spike</td>\n",
       "      <td>L981F</td>\n",
       "      <td>981.0</td>\n",
       "      <td>L</td>\n",
       "      <td>F</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>nuc:C25000T</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>B.1.1.529</td>\n",
       "      <td>nuc</td>\n",
       "      <td>C25000T</td>\n",
       "      <td>25000.0</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>spike:G142D</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>G142D</td>\n",
       "      <td>142.0</td>\n",
       "      <td>G</td>\n",
       "      <td>D</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>spike:G339D</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>G339D</td>\n",
       "      <td>339.0</td>\n",
       "      <td>G</td>\n",
       "      <td>D</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>spike:S373P</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S373P</td>\n",
       "      <td>373.0</td>\n",
       "      <td>S</td>\n",
       "      <td>P</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>spike:S375F</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S375F</td>\n",
       "      <td>375.0</td>\n",
       "      <td>S</td>\n",
       "      <td>F</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>spike:K417N</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>K417N</td>\n",
       "      <td>417.0</td>\n",
       "      <td>K</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>spike:N440K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N440K</td>\n",
       "      <td>440.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>spike:S477N</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>S477N</td>\n",
       "      <td>477.0</td>\n",
       "      <td>S</td>\n",
       "      <td>N</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>spike:T478K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>T478K</td>\n",
       "      <td>478.0</td>\n",
       "      <td>T</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>spike:E484A</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>E484A</td>\n",
       "      <td>484.0</td>\n",
       "      <td>E</td>\n",
       "      <td>A</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>spike:Q493R</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q493R</td>\n",
       "      <td>493.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>spike:Q498R</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q498R</td>\n",
       "      <td>498.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>R</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>spike:N501Y</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N501Y</td>\n",
       "      <td>501.0</td>\n",
       "      <td>N</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>spike:Y505H</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Y505H</td>\n",
       "      <td>505.0</td>\n",
       "      <td>Y</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>spike:D614G</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D614G</td>\n",
       "      <td>614.0</td>\n",
       "      <td>D</td>\n",
       "      <td>G</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>spike:H655Y</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>H655Y</td>\n",
       "      <td>655.0</td>\n",
       "      <td>H</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>spike:N679K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N679K</td>\n",
       "      <td>679.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>spike:P681H</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>P681H</td>\n",
       "      <td>681.0</td>\n",
       "      <td>P</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>spike:N764K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N764K</td>\n",
       "      <td>764.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>spike:D796Y</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>D796Y</td>\n",
       "      <td>796.0</td>\n",
       "      <td>D</td>\n",
       "      <td>Y</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>spike:Q954H</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>Q954H</td>\n",
       "      <td>954.0</td>\n",
       "      <td>Q</td>\n",
       "      <td>H</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>spike:N969K</td>\n",
       "      <td>BA.1</td>\n",
       "      <td>None</td>\n",
       "      <td>spike</td>\n",
       "      <td>N969K</td>\n",
       "      <td>969.0</td>\n",
       "      <td>N</td>\n",
       "      <td>K</td>\n",
       "      <td>S</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          sites lineage parent_lineage protein mutation  position reference  \\\n",
       "8    spike:A67V    BA.1      B.1.1.529   spike     A67V      67.0         A   \n",
       "9   del:21765:6    BA.1      B.1.1.529     del    21765   21765.0             \n",
       "10   spike:T95I    BA.1      B.1.1.529   spike     T95I      95.0         T   \n",
       "11  del:21987:9    BA.1      B.1.1.529     del    21987   21987.0             \n",
       "12  del:22194:3    BA.1      B.1.1.529     del    22194   22194.0             \n",
       "14  spike:S371L    BA.1      B.1.1.529   spike    S371L     371.0         S   \n",
       "15  spike:G446S    BA.1      B.1.1.529   spike    G446S     446.0         G   \n",
       "16  spike:G496S    BA.1      B.1.1.529   spike    G496S     496.0         G   \n",
       "17  spike:T547K    BA.1      B.1.1.529   spike    T547K     547.0         T   \n",
       "18  spike:N856K    BA.1      B.1.1.529   spike    N856K     856.0         N   \n",
       "19  spike:L981F    BA.1      B.1.1.529   spike    L981F     981.0         L   \n",
       "20  nuc:C25000T    BA.1      B.1.1.529     nuc  C25000T   25000.0         C   \n",
       "6   spike:G142D    BA.1           None   spike    G142D     142.0         G   \n",
       "7   spike:G339D    BA.1           None   spike    G339D     339.0         G   \n",
       "8   spike:S373P    BA.1           None   spike    S373P     373.0         S   \n",
       "9   spike:S375F    BA.1           None   spike    S375F     375.0         S   \n",
       "10  spike:K417N    BA.1           None   spike    K417N     417.0         K   \n",
       "11  spike:N440K    BA.1           None   spike    N440K     440.0         N   \n",
       "12  spike:S477N    BA.1           None   spike    S477N     477.0         S   \n",
       "13  spike:T478K    BA.1           None   spike    T478K     478.0         T   \n",
       "14  spike:E484A    BA.1           None   spike    E484A     484.0         E   \n",
       "15  spike:Q493R    BA.1           None   spike    Q493R     493.0         Q   \n",
       "16  spike:Q498R    BA.1           None   spike    Q498R     498.0         Q   \n",
       "17  spike:N501Y    BA.1           None   spike    N501Y     501.0         N   \n",
       "18  spike:Y505H    BA.1           None   spike    Y505H     505.0         Y   \n",
       "19  spike:D614G    BA.1           None   spike    D614G     614.0         D   \n",
       "20  spike:H655Y    BA.1           None   spike    H655Y     655.0         H   \n",
       "21  spike:N679K    BA.1           None   spike    N679K     679.0         N   \n",
       "22  spike:P681H    BA.1           None   spike    P681H     681.0         P   \n",
       "23  spike:N764K    BA.1           None   spike    N764K     764.0         N   \n",
       "24  spike:D796Y    BA.1           None   spike    D796Y     796.0         D   \n",
       "25  spike:Q954H    BA.1           None   spike    Q954H     954.0         Q   \n",
       "26  spike:N969K    BA.1           None   spike    N969K     969.0         N   \n",
       "\n",
       "   alternate protein_normalized  removal_aromatic  removal_large  \\\n",
       "8          V                  S             False          False   \n",
       "9                             S             False          False   \n",
       "10         I                  S             False          False   \n",
       "11                            S             False          False   \n",
       "12                            S             False          False   \n",
       "14         L                  S             False          False   \n",
       "15         S                  S             False          False   \n",
       "16         S                  S             False          False   \n",
       "17         K                  S             False          False   \n",
       "18         K                  S             False          False   \n",
       "19         F                  S             False           True   \n",
       "20         T                  S             False          False   \n",
       "6          D                  S             False          False   \n",
       "7          D                  S             False          False   \n",
       "8          P                  S             False          False   \n",
       "9          F                  S             False          False   \n",
       "10         N                  S             False           True   \n",
       "11         K                  S             False          False   \n",
       "12         N                  S             False          False   \n",
       "13         K                  S             False          False   \n",
       "14         A                  S             False          False   \n",
       "15         R                  S             False          False   \n",
       "16         R                  S             False          False   \n",
       "17         Y                  S             False          False   \n",
       "18         H                  S             False          False   \n",
       "19         G                  S             False          False   \n",
       "20         Y                  S             False          False   \n",
       "21         K                  S             False          False   \n",
       "22         H                  S             False          False   \n",
       "23         K                  S             False          False   \n",
       "24         Y                  S             False          False   \n",
       "25         H                  S             False          False   \n",
       "26         K                  S             False          False   \n",
       "\n",
       "    add_aromatic  add_large  count  \n",
       "8          False      False   True  \n",
       "9          False      False   True  \n",
       "10         False       True   True  \n",
       "11         False      False   True  \n",
       "12         False      False   True  \n",
       "14         False       True   True  \n",
       "15         False      False   True  \n",
       "16         False      False   True  \n",
       "17         False       True   True  \n",
       "18         False       True   True  \n",
       "19          True      False   True  \n",
       "20         False      False   True  \n",
       "6          False      False   True  \n",
       "7          False      False   True  \n",
       "8          False      False   True  \n",
       "9           True      False   True  \n",
       "10         False      False   True  \n",
       "11         False       True   True  \n",
       "12         False      False   True  \n",
       "13         False       True   True  \n",
       "14         False      False   True  \n",
       "15         False       True   True  \n",
       "16         False       True   True  \n",
       "17          True      False   True  \n",
       "18         False      False   True  \n",
       "19         False      False   True  \n",
       "20         False      False   True  \n",
       "21         False       True   True  \n",
       "22          True      False   True  \n",
       "23         False       True   True  \n",
       "24          True      False   True  \n",
       "25          True      False   True  \n",
       "26         False       True   True  "
      ]
     },
     "execution_count": 278,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lineages[(lineages.lineage == \"BA.1\") & (lineages.protein_normalized == \"S\")]"
   ]
  }
 ],
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