tcrex.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import Levenshtein as lev\n",
    "from tqdm import tqdm_notebook"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>CDR3_beta</th>\n",
       "      <th>TRBJ_gene</th>\n",
       "      <th>TRBV_gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CASSLLGISTYNEQFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CASSLIGVSSYNEQFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CASSDRDRGHYEQYF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CASSSRDIGFYEQYF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CASSIGTGIYNEQFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          CDR3_beta TRBJ_gene TRBV_gene\n",
       "0  CASSLLGISTYNEQFF   TRBV7-9   TRBJ2-1\n",
       "1  CASSLIGVSSYNEQFF   TRBV7-9   TRBJ2-1\n",
       "2   CASSDRDRGHYEQYF   TRBV7-9   TRBJ2-7\n",
       "3   CASSSRDIGFYEQYF   TRBV7-9   TRBJ2-7\n",
       "4   CASSIGTGIYNEQFF   TRBV7-9   TRBJ2-1"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cols = [\"CDR3.sequence\", \"V.gene\", \"J.gene\"]\n",
    "new_cols = [\"CDR3_beta\", 'TRBJ_gene', 'TRBV_gene']\n",
    "df_trp = pd.read_table(\"data/GSM3155095_P01_TPRstim_CD8_beta.txt.gz\")[cols]\n",
    "df_all = pd.read_table(\"data/GSM3155090_P01_unstim_CD8_beta.txt.gz\")[cols]\n",
    "df_trp.columns = new_cols\n",
    "df_all.columns = new_cols\n",
    "\n",
    "df_trp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a689762430f5449d955fb09974a69b6e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(IntProgress(value=0, max=584630), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1001\n"
     ]
    }
   ],
   "source": [
    "candidates = []\n",
    "for source_i in tqdm_notebook(range(len(df_all))):\n",
    "    source_seq = df_all[\"CDR3_beta\"][0]\n",
    "    for i in range(len(df_trp)):\n",
    "        if lev.distance(source_seq, df_trp[\"CDR3_beta\"][i]) == 1:\n",
    "            candidates.append(source_i)\n",
    "            break\n",
    "    if len(candidates) > 1000:\n",
    "        break\n",
    "        \n",
    "print(len(candidates))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\n"
     ]
    }
   ],
   "source": [
    "# good - CASSLRGESSYNEQFF\n",
    "# bad - CASSLSSGTRVLGEQFF\n",
    "# bad - CASSLSSVLAGGLSTDTQYF\n",
    "# bad - CASSYQGYEQYF\n",
    "candidates = []\n",
    "source_seq = \"CASSLRGESSYNEQFF\"\n",
    "for i in range(len(df_trp)):\n",
    "    if lev.distance(source_seq, df_trp[\"CDR3_beta\"][i]) == 1:\n",
    "        candidates.append(source_i)\n",
    "        break\n",
    "        \n",
    "print(len(candidates))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_all.loc[candidates, :].to_csv(\"tcrex.tsv\", sep=\"\\t\", index=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "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>CDR3_beta</th>\n",
       "      <th>TRBV_gene</th>\n",
       "      <th>TRBJ_gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CASSWDTPGDEQYF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CASSQDSSSGGNNEQFF</td>\n",
       "      <td>TRBV4-2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CASSPRAGANTGELFF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CASTPTQLDYEQYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CASSLGDVTPTGLGSGYTF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>CASSSPEPNTEAFF</td>\n",
       "      <td>TRBV6-2/6-3</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CASSLLGISTYNEQFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CASGLVSVIGAVPYNEQFF</td>\n",
       "      <td>TRBV12-5</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>CASSLTDKIDTQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CASSSVLNAYEQYF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>CASSYLYPDRDREGYTF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>CASSPTSGLSGANVLTF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>CASSLRGASGRPEGETQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>CASHGTSAPYRYEQYF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>CASSLNSRAGRGAEAFF</td>\n",
       "      <td>TRBV11-2</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>CASSSGRRNTEAFF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>CASSEFRSRGQQETQYF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>CASSWLIVGTEQYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>CASSQGRSYEQYF</td>\n",
       "      <td>TRBV14</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>CASSLGLAGGVSTDTQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>CASSSLSLLGGERSYNEQFF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>CASSLFSTAGNEQFF</td>\n",
       "      <td>TRBV5-1</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>CASSAEGGHEQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>CASSHPRIFSYGYTF</td>\n",
       "      <td>TRBV11-2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>CASSQEIGGLAYNEQFF</td>\n",
       "      <td>TRBV4-2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>CASPQGGQGGGTEAFF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>CASSRGGAPNSPLHF</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ1-6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>CASSSSSEAFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>CASGRGDSEAFF</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>CASSLSQARPQHF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584600</th>\n",
       "      <td>CAWKAFF</td>\n",
       "      <td>TRBV30</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584601</th>\n",
       "      <td>CAGQNTF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584602</th>\n",
       "      <td>CATPFDF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584603</th>\n",
       "      <td>CATPRYF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584604</th>\n",
       "      <td>CATTPGF</td>\n",
       "      <td>TRBV24-1</td>\n",
       "      <td>TRBJ2-4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584605</th>\n",
       "      <td>CASPADF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584606</th>\n",
       "      <td>CASPEAF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584607</th>\n",
       "      <td>CASGGYF</td>\n",
       "      <td>TRBV27</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584608</th>\n",
       "      <td>CASEQFF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584609</th>\n",
       "      <td>CASSSNF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584610</th>\n",
       "      <td>CASSSNA</td>\n",
       "      <td>TRBV11-1</td>\n",
       "      <td>TRBJ1-4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584611</th>\n",
       "      <td>CASSAHF</td>\n",
       "      <td>TRBV9</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584612</th>\n",
       "      <td>CASRQFF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584613</th>\n",
       "      <td>CASNRIF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584614</th>\n",
       "      <td>CASKRCC</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584615</th>\n",
       "      <td>CARIPYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584616</th>\n",
       "      <td>CASQGIF</td>\n",
       "      <td>TRBV5-1</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584617</th>\n",
       "      <td>CGAEAFF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584618</th>\n",
       "      <td>CSAAGFF</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584619</th>\n",
       "      <td>CSARFAL</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584620</th>\n",
       "      <td>CSVEGYF</td>\n",
       "      <td>TRBV29-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584621</th>\n",
       "      <td>YSVVGLF</td>\n",
       "      <td>TRBV29-1</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584622</th>\n",
       "      <td>CASSPG</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584623</th>\n",
       "      <td>CANKHF</td>\n",
       "      <td>TRBV23-1</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584624</th>\n",
       "      <td>CAAYF</td>\n",
       "      <td>TRBV24-1</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584625</th>\n",
       "      <td>CASNV</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584626</th>\n",
       "      <td>CSAPL</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584627</th>\n",
       "      <td>CRDYF</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584628</th>\n",
       "      <td>CASS</td>\n",
       "      <td>TRBV25-1</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584629</th>\n",
       "      <td>CASL</td>\n",
       "      <td>TRBV4-1</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>584630 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  CDR3_beta        TRBV_gene TRBJ_gene\n",
       "0            CASSWDTPGDEQYF          TRBV7-8   TRBJ2-7\n",
       "1         CASSQDSSSGGNNEQFF          TRBV4-2   TRBJ2-1\n",
       "2          CASSPRAGANTGELFF          TRBV7-8   TRBJ2-2\n",
       "3            CASTPTQLDYEQYF           TRBV28   TRBJ2-7\n",
       "4       CASSLGDVTPTGLGSGYTF          TRBV7-2   TRBJ1-2\n",
       "...                     ...              ...       ...\n",
       "584625                CASNV  TRBV6-1/6-5/6-6   TRBJ1-2\n",
       "584626                CSAPL         TRBV20-1   TRBJ2-7\n",
       "584627                CRDYF         TRBV20-1   TRBJ2-7\n",
       "584628                 CASS         TRBV25-1   TRBJ1-1\n",
       "584629                 CASL          TRBV4-1   TRBJ1-1\n",
       "\n",
       "[584630 rows x 3 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_cols = [\"CDR3_beta\", 'TRBV_gene', 'TRBJ_gene']\n",
    "df_all.columns = new_cols\n",
    "df_all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "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>CDR3_beta</th>\n",
       "      <th>TRBJ_gene</th>\n",
       "      <th>TRBV_gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CASSWDTPGDEQYF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CASSQDSSSGGNNEQFF</td>\n",
       "      <td>TRBV4-2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CASSPRAGANTGELFF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CASTPTQLDYEQYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>CASSLGDVTPTGLGSGYTF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>CASSSPEPNTEAFF</td>\n",
       "      <td>TRBV6-2/6-3</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CASSLLGISTYNEQFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CASGLVSVIGAVPYNEQFF</td>\n",
       "      <td>TRBV12-5</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>CASSLTDKIDTQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CASSSVLNAYEQYF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>CASSYLYPDRDREGYTF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>CASSPTSGLSGANVLTF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ2-6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>CASSLRGASGRPEGETQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>CASHGTSAPYRYEQYF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>CASSLNSRAGRGAEAFF</td>\n",
       "      <td>TRBV11-2</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>CASSSGRRNTEAFF</td>\n",
       "      <td>TRBV7-8</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>CASSEFRSRGQQETQYF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>CASSWLIVGTEQYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>CASSQGRSYEQYF</td>\n",
       "      <td>TRBV14</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>CASSLGLAGGVSTDTQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>CASSSLSLLGGERSYNEQFF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>CASSLFSTAGNEQFF</td>\n",
       "      <td>TRBV5-1</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>CASSAEGGHEQYF</td>\n",
       "      <td>TRBV7-2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>CASSHPRIFSYGYTF</td>\n",
       "      <td>TRBV11-2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>CASSQEIGGLAYNEQFF</td>\n",
       "      <td>TRBV4-2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>CASPQGGQGGGTEAFF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>CASSRGGAPNSPLHF</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ1-6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>CASSSSSEAFF</td>\n",
       "      <td>TRBV7-9</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>CASGRGDSEAFF</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>CASSLSQARPQHF</td>\n",
       "      <td>TRBV12-3/12-4</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584600</th>\n",
       "      <td>CAWKAFF</td>\n",
       "      <td>TRBV30</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584601</th>\n",
       "      <td>CAGQNTF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584602</th>\n",
       "      <td>CATPFDF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584603</th>\n",
       "      <td>CATPRYF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584604</th>\n",
       "      <td>CATTPGF</td>\n",
       "      <td>TRBV24-1</td>\n",
       "      <td>TRBJ2-4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584605</th>\n",
       "      <td>CASPADF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ2-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584606</th>\n",
       "      <td>CASPEAF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584607</th>\n",
       "      <td>CASGGYF</td>\n",
       "      <td>TRBV27</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584608</th>\n",
       "      <td>CASEQFF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584609</th>\n",
       "      <td>CASSSNF</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584610</th>\n",
       "      <td>CASSSNA</td>\n",
       "      <td>TRBV11-1</td>\n",
       "      <td>TRBJ1-4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584611</th>\n",
       "      <td>CASSAHF</td>\n",
       "      <td>TRBV9</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584612</th>\n",
       "      <td>CASRQFF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584613</th>\n",
       "      <td>CASNRIF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584614</th>\n",
       "      <td>CASKRCC</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584615</th>\n",
       "      <td>CARIPYF</td>\n",
       "      <td>TRBV28</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584616</th>\n",
       "      <td>CASQGIF</td>\n",
       "      <td>TRBV5-1</td>\n",
       "      <td>TRBJ2-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584617</th>\n",
       "      <td>CGAEAFF</td>\n",
       "      <td>TRBV2</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584618</th>\n",
       "      <td>CSAAGFF</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584619</th>\n",
       "      <td>CSARFAL</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584620</th>\n",
       "      <td>CSVEGYF</td>\n",
       "      <td>TRBV29-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584621</th>\n",
       "      <td>YSVVGLF</td>\n",
       "      <td>TRBV29-1</td>\n",
       "      <td>TRBJ2-3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584622</th>\n",
       "      <td>CASSPG</td>\n",
       "      <td>TRBV5-4</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584623</th>\n",
       "      <td>CANKHF</td>\n",
       "      <td>TRBV23-1</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584624</th>\n",
       "      <td>CAAYF</td>\n",
       "      <td>TRBV24-1</td>\n",
       "      <td>TRBJ1-5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584625</th>\n",
       "      <td>CASNV</td>\n",
       "      <td>TRBV6-1/6-5/6-6</td>\n",
       "      <td>TRBJ1-2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584626</th>\n",
       "      <td>CSAPL</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584627</th>\n",
       "      <td>CRDYF</td>\n",
       "      <td>TRBV20-1</td>\n",
       "      <td>TRBJ2-7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584628</th>\n",
       "      <td>CASS</td>\n",
       "      <td>TRBV25-1</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584629</th>\n",
       "      <td>CASL</td>\n",
       "      <td>TRBV4-1</td>\n",
       "      <td>TRBJ1-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>584630 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  CDR3_beta        TRBJ_gene TRBV_gene\n",
       "0            CASSWDTPGDEQYF          TRBV7-8   TRBJ2-7\n",
       "1         CASSQDSSSGGNNEQFF          TRBV4-2   TRBJ2-1\n",
       "2          CASSPRAGANTGELFF          TRBV7-8   TRBJ2-2\n",
       "3            CASTPTQLDYEQYF           TRBV28   TRBJ2-7\n",
       "4       CASSLGDVTPTGLGSGYTF          TRBV7-2   TRBJ1-2\n",
       "...                     ...              ...       ...\n",
       "584625                CASNV  TRBV6-1/6-5/6-6   TRBJ1-2\n",
       "584626                CSAPL         TRBV20-1   TRBJ2-7\n",
       "584627                CRDYF         TRBV20-1   TRBJ2-7\n",
       "584628                 CASS         TRBV25-1   TRBJ1-1\n",
       "584629                 CASL          TRBV4-1   TRBJ1-1\n",
       "\n",
       "[584630 rows x 3 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_all"
   ]
  }
 ],
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