one_hot encode and physiochemical encode.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 49,
   "id": "63d41b6e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "from sklearn.preprocessing import OneHotEncoder\n",
    "from sklearn.preprocessing import LabelEncoder\n",
    "import matplotlib\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "c2c18a2b-d71e-4359-b4e2-2fbd03be1843",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/cherylliu/opt/anaconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3165: DtypeWarning: Columns (5,8,44,45,94,95,104,107,109,125,126,127,128,143,144,155,191,193,194) have mixed types.Specify dtype option on import or set low_memory=False.\n",
      "  has_raised = await self.run_ast_nodes(code_ast.body, cell_name,\n"
     ]
    }
   ],
   "source": [
    "df = pd.read_csv(\"all.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "id": "3633fa61-5c3f-4b0f-9601-a553dcb9ae40",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence_id_heavy</th>\n",
       "      <th>sequence_heavy</th>\n",
       "      <th>locus_heavy</th>\n",
       "      <th>stop_codon_heavy</th>\n",
       "      <th>vj_in_frame_heavy</th>\n",
       "      <th>v_frameshift_heavy</th>\n",
       "      <th>productive_heavy</th>\n",
       "      <th>rev_comp_heavy</th>\n",
       "      <th>complete_vdj_heavy</th>\n",
       "      <th>v_call_heavy</th>\n",
       "      <th>...</th>\n",
       "      <th>cdr3_end_light</th>\n",
       "      <th>np1_light</th>\n",
       "      <th>np1_length_light</th>\n",
       "      <th>np2_light</th>\n",
       "      <th>np2_length_light</th>\n",
       "      <th>c_region_light</th>\n",
       "      <th>Isotype_light</th>\n",
       "      <th>Redundancy_light</th>\n",
       "      <th>ANARCI_numbering_light</th>\n",
       "      <th>ANARCI_status_light</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AAACCTGAGAACTCGG-1_contig_2</td>\n",
       "      <td>GGCTTTCTGAGAGTCATGGACCTCCTGCACAAGAACATGAAACACC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
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       "      <td>T</td>\n",
       "      <td>IGHV4-34*01</td>\n",
       "      <td>...</td>\n",
       "      <td>411.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AAACCTGAGATATGGT-1_contig_2</td>\n",
       "      <td>AGCTCTGGGAGAGGAGCTCCAGCCTTGGGATTCCCAGCTGTCTCCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-73*02</td>\n",
       "      <td>...</td>\n",
       "      <td>404.0</td>\n",
       "      <td>GCTGC</td>\n",
       "      <td>5.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AAACCTGAGATGTCGG-1_contig_2</td>\n",
       "      <td>TGGGGACCCAAAAACCACACCCCTCCTTGGGAGAATCCCCTAGATC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-18*01</td>\n",
       "      <td>...</td>\n",
       "      <td>388.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'S', '3 ': 'E', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AAACCTGAGCACCGTC-1_contig_2</td>\n",
       "      <td>ACCCAAAAACCACACCCCTCCTTGGGAGAATCCCCTAGATCACAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-18*01</td>\n",
       "      <td>...</td>\n",
       "      <td>398.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AAACCTGAGCGTAATA-1_contig_2</td>\n",
       "      <td>AGCTCTGGGAGAGGAGCCCCAGCCGTGAGATTCCCAGGAGTTTCCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-49*04</td>\n",
       "      <td>...</td>\n",
       "      <td>385.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAACGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'Q', '2 ': 'L', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 198 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             sequence_id_heavy  \\\n",
       "0  AAACCTGAGAACTCGG-1_contig_2   \n",
       "1  AAACCTGAGATATGGT-1_contig_2   \n",
       "2  AAACCTGAGATGTCGG-1_contig_2   \n",
       "3  AAACCTGAGCACCGTC-1_contig_2   \n",
       "4  AAACCTGAGCGTAATA-1_contig_2   \n",
       "\n",
       "                                      sequence_heavy locus_heavy  \\\n",
       "0  GGCTTTCTGAGAGTCATGGACCTCCTGCACAAGAACATGAAACACC...           H   \n",
       "1  AGCTCTGGGAGAGGAGCTCCAGCCTTGGGATTCCCAGCTGTCTCCA...           H   \n",
       "2  TGGGGACCCAAAAACCACACCCCTCCTTGGGAGAATCCCCTAGATC...           H   \n",
       "3  ACCCAAAAACCACACCCCTCCTTGGGAGAATCCCCTAGATCACAGC...           H   \n",
       "4  AGCTCTGGGAGAGGAGCCCCAGCCGTGAGATTCCCAGGAGTTTCCA...           H   \n",
       "\n",
       "  stop_codon_heavy vj_in_frame_heavy v_frameshift_heavy productive_heavy  \\\n",
       "0                F                 T                  F                T   \n",
       "1                F                 T                  F                T   \n",
       "2                F                 T                  F                T   \n",
       "3                F                 T                  F                T   \n",
       "4                F                 T                  F                T   \n",
       "\n",
       "  rev_comp_heavy complete_vdj_heavy v_call_heavy  ... cdr3_end_light  \\\n",
       "0              F                  T  IGHV4-34*01  ...          411.0   \n",
       "1              F                  T  IGHV3-73*02  ...          404.0   \n",
       "2              F                  T  IGHV1-18*01  ...          388.0   \n",
       "3              F                  T  IGHV1-18*01  ...          398.0   \n",
       "4              F                  T  IGHV3-49*04  ...          385.0   \n",
       "\n",
       "  np1_light np1_length_light np2_light np2_length_light  \\\n",
       "0       NaN              0.0       NaN              NaN   \n",
       "1     GCTGC              5.0       NaN              NaN   \n",
       "2       NaN              0.0       NaN              NaN   \n",
       "3       NaN              0.0       NaN              NaN   \n",
       "4       NaN              0.0       NaN              NaN   \n",
       "\n",
       "                                      c_region_light  Isotype_light  \\\n",
       "0  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...           Bulk   \n",
       "1  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...           Bulk   \n",
       "2  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...           Bulk   \n",
       "3  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...           Bulk   \n",
       "4  GTCAGCCCAACGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...           Bulk   \n",
       "\n",
       "   Redundancy_light                             ANARCI_numbering_light  \\\n",
       "0               1.0  {'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...   \n",
       "1               1.0  {'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...   \n",
       "2               1.0  {'fwl1': {'1 ': 'S', '2 ': 'S', '3 ': 'E', '4 ...   \n",
       "3               1.0  {'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "4               1.0  {'fwl1': {'1 ': 'Q', '2 ': 'L', '3 ': 'V', '4 ...   \n",
       "\n",
       "   ANARCI_status_light  \n",
       "0                |||||  \n",
       "1                |||||  \n",
       "2                |||||  \n",
       "3                |||||  \n",
       "4                |||||  \n",
       "\n",
       "[5 rows x 198 columns]"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "id": "f17cb30f-76db-4a6e-87c5-3388943b0fc8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['sequence_id_heavy', 'sequence_heavy', 'locus_heavy',\n",
       "       'stop_codon_heavy', 'vj_in_frame_heavy', 'v_frameshift_heavy',\n",
       "       'productive_heavy', 'rev_comp_heavy', 'complete_vdj_heavy',\n",
       "       'v_call_heavy',\n",
       "       ...\n",
       "       'cdr3_end_light', 'np1_light', 'np1_length_light', 'np2_light',\n",
       "       'np2_length_light', 'c_region_light', 'Isotype_light',\n",
       "       'Redundancy_light', 'ANARCI_numbering_light', 'ANARCI_status_light'],\n",
       "      dtype='object', length=198)"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "id": "1d1feb27-9386-4906-b8df-43c17e829de1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1572406, 198)"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "id": "5f222e24-bd73-4c87-8399-f6f76924242c",
   "metadata": {},
   "outputs": [],
   "source": [
    "#random \n",
    "small_df = df.sample(n = 1000, random_state = 48, replace = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "id": "8a7847eb-754c-4798-8b0a-a2e031447b03",
   "metadata": {},
   "outputs": [],
   "source": [
    "#small_df = pd.read_csv(\"datasets/1279050_1_Paired_All.csv.gz\", compression=\"gzip\", sep=\",\", skiprows=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "id": "4818e98a",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>sequence_id_heavy</th>\n",
       "      <th>sequence_heavy</th>\n",
       "      <th>locus_heavy</th>\n",
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       "      <th>...</th>\n",
       "      <th>cdr3_end_light</th>\n",
       "      <th>np1_light</th>\n",
       "      <th>np1_length_light</th>\n",
       "      <th>np2_light</th>\n",
       "      <th>np2_length_light</th>\n",
       "      <th>c_region_light</th>\n",
       "      <th>Isotype_light</th>\n",
       "      <th>Redundancy_light</th>\n",
       "      <th>ANARCI_numbering_light</th>\n",
       "      <th>ANARCI_status_light</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1537568</th>\n",
       "      <td>AACTCAGAGTTGTAGA-1_contig_1</td>\n",
       "      <td>ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-69*01</td>\n",
       "      <td>...</td>\n",
       "      <td>389.0</td>\n",
       "      <td>GGGG</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...</td>\n",
       "      <td>|||||</td>\n",
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       "    <tr>\n",
       "      <th>1390188</th>\n",
       "      <td>TGCCAAACAATCACAC-1_contig_1</td>\n",
       "      <td>TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-38-2*02</td>\n",
       "      <td>...</td>\n",
       "      <td>394.0</td>\n",
       "      <td>AA</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>413004</th>\n",
       "      <td>AGTCTTTCATTGGGCC-1_contig_1</td>\n",
       "      <td>ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-59*01</td>\n",
       "      <td>...</td>\n",
       "      <td>399.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
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       "    <tr>\n",
       "      <th>260850</th>\n",
       "      <td>CATCCACAGTGAAGTT-1_contig_1</td>\n",
       "      <td>GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-21*01</td>\n",
       "      <td>...</td>\n",
       "      <td>396.0</td>\n",
       "      <td>TT</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
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       "    <tr>\n",
       "      <th>981594</th>\n",
       "      <td>GACGGCTTCTTCTGGC-1_contig_2</td>\n",
       "      <td>CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-30*04</td>\n",
       "      <td>...</td>\n",
       "      <td>399.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 198 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence_id_heavy  \\\n",
       "1537568  AACTCAGAGTTGTAGA-1_contig_1   \n",
       "1390188  TGCCAAACAATCACAC-1_contig_1   \n",
       "413004   AGTCTTTCATTGGGCC-1_contig_1   \n",
       "260850   CATCCACAGTGAAGTT-1_contig_1   \n",
       "981594   GACGGCTTCTTCTGGC-1_contig_2   \n",
       "\n",
       "                                            sequence_heavy locus_heavy  \\\n",
       "1537568  ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...           H   \n",
       "1390188  TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...           H   \n",
       "413004   ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...           H   \n",
       "260850   GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...           H   \n",
       "981594   CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...           H   \n",
       "\n",
       "        stop_codon_heavy vj_in_frame_heavy v_frameshift_heavy  \\\n",
       "1537568                F                 T                  F   \n",
       "1390188                F                 T                  F   \n",
       "413004                 F                 T                  F   \n",
       "260850                 F                 T                  F   \n",
       "981594                 F                 T                  F   \n",
       "\n",
       "        productive_heavy rev_comp_heavy complete_vdj_heavy   v_call_heavy  \\\n",
       "1537568                T              F                  T    IGHV1-69*01   \n",
       "1390188                T              F                  T  IGHV4-38-2*02   \n",
       "413004                 T              F                  T    IGHV4-59*01   \n",
       "260850                 T              F                  T    IGHV3-21*01   \n",
       "981594                 T              F                  T    IGHV3-30*04   \n",
       "\n",
       "         ... cdr3_end_light np1_light np1_length_light np2_light  \\\n",
       "1537568  ...          389.0      GGGG              4.0       NaN   \n",
       "1390188  ...          394.0        AA              2.0       NaN   \n",
       "413004   ...          399.0       NaN              0.0       NaN   \n",
       "260850   ...          396.0        TT              2.0       NaN   \n",
       "981594   ...          399.0       NaN              0.0       NaN   \n",
       "\n",
       "        np2_length_light                                     c_region_light  \\\n",
       "1537568              NaN  GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...   \n",
       "1390188              NaN  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...   \n",
       "413004               NaN  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...   \n",
       "260850               NaN  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...   \n",
       "981594               NaN  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...   \n",
       "\n",
       "         Isotype_light  Redundancy_light  \\\n",
       "1537568           Bulk               1.0   \n",
       "1390188           Bulk               1.0   \n",
       "413004            Bulk               1.0   \n",
       "260850            Bulk               1.0   \n",
       "981594            Bulk               1.0   \n",
       "\n",
       "                                    ANARCI_numbering_light  \\\n",
       "1537568  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...   \n",
       "1390188  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...   \n",
       "413004   {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "260850   {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "981594   {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "\n",
       "         ANARCI_status_light  \n",
       "1537568                |||||  \n",
       "1390188                |||||  \n",
       "413004                 |||||  \n",
       "260850                 |||||  \n",
       "981594                 |||||  \n",
       "\n",
       "[5 rows x 198 columns]"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "small_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d11c4d87-e61c-4ae3-8e53-5e3474768d4e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "id": "b73ed175",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(1000, 198)"
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "small_df.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bbe97119",
   "metadata": {},
   "source": [
    "**label encoding test**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "id": "d40deb2d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1537568    QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLE...\n",
       "1390188    QVQLQESGPGLVKPSETLSLTCAVSGYSISSGYYWGWIRQPPGKGL...\n",
       "413004     QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLE...\n",
       "260850     EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLE...\n",
       "981594     QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYAMHWVRQAPGKGLE...\n",
       "                                 ...                        \n",
       "1175461    QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLE...\n",
       "1535695    QVQLQESGPGLVKPSETLSLTCAVSGHSISSGYYWGWIRQPPGKGL...\n",
       "361113     QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGSYYWSWIRQPPGKG...\n",
       "748949     QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLE...\n",
       "839076     QVHLVESGGGLANPGGSLTLSCVGSGFTFSDHYMTWLRQAPGEGLE...\n",
       "Name: sequence_alignment_aa_heavy, Length: 1000, dtype: object"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "small_df['sequence_alignment_aa_heavy']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "id": "8cac6994",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "LabelEncoder()"
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "le = LabelEncoder()\n",
    "le.fit(small_df[\"sequence_alignment_aa_heavy\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "id": "17cbcfaf",
   "metadata": {},
   "outputs": [],
   "source": [
    "integer_encoded_letters_array = le.transform(small_df[\"sequence_alignment_aa_heavy\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "id": "098d14e5",
   "metadata": {},
   "outputs": [],
   "source": [
    "#integer_encoded_letters_array"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "id": "7f15eabc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1000"
      ]
     },
     "execution_count": 62,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(integer_encoded_letters_array)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "id": "eb774a4b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#1d to 2d\n",
    "\n",
    "# integer_encoded_letters_array = integer_encoded_letters_array.reshape(len(integer_encoded_letters_array), 1)\n",
    "# integer_encoded_letters_array"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "id": "ce943c74",
   "metadata": {},
   "outputs": [],
   "source": [
    "#convert to original sequences\n",
    "original_letters = le.inverse_transform(integer_encoded_letters_array)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "id": "cbc750fe",
   "metadata": {},
   "outputs": [],
   "source": [
    "#change array to series\n",
    "integer_encoded_letters_series = pd.Series(integer_encoded_letters_array)\n",
    "integer_encoded_letters_series\n",
    "#add to small_df\n",
    "small_df['integer_encoded_letters'] = integer_encoded_letters_series"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e9783804",
   "metadata": {},
   "source": [
    "**one hot encode test**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "id": "7bca0a7a",
   "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>sequence_id_heavy</th>\n",
       "      <th>sequence_heavy</th>\n",
       "      <th>locus_heavy</th>\n",
       "      <th>stop_codon_heavy</th>\n",
       "      <th>vj_in_frame_heavy</th>\n",
       "      <th>v_frameshift_heavy</th>\n",
       "      <th>productive_heavy</th>\n",
       "      <th>rev_comp_heavy</th>\n",
       "      <th>complete_vdj_heavy</th>\n",
       "      <th>v_call_heavy</th>\n",
       "      <th>...</th>\n",
       "      <th>np1_length_light</th>\n",
       "      <th>np2_light</th>\n",
       "      <th>np2_length_light</th>\n",
       "      <th>c_region_light</th>\n",
       "      <th>Isotype_light</th>\n",
       "      <th>Redundancy_light</th>\n",
       "      <th>ANARCI_numbering_light</th>\n",
       "      <th>ANARCI_status_light</th>\n",
       "      <th>integer_encoded_letters_392.0</th>\n",
       "      <th>integer_encoded_letters_719.0</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1537568</th>\n",
       "      <td>AACTCAGAGTTGTAGA-1_contig_1</td>\n",
       "      <td>ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-69*01</td>\n",
       "      <td>...</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1390188</th>\n",
       "      <td>TGCCAAACAATCACAC-1_contig_1</td>\n",
       "      <td>TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-38-2*02</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>413004</th>\n",
       "      <td>AGTCTTTCATTGGGCC-1_contig_1</td>\n",
       "      <td>ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-59*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>260850</th>\n",
       "      <td>CATCCACAGTGAAGTT-1_contig_1</td>\n",
       "      <td>GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-21*01</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>981594</th>\n",
       "      <td>GACGGCTTCTTCTGGC-1_contig_2</td>\n",
       "      <td>CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-30*04</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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",
       "      <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",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1175461</th>\n",
       "      <td>AGAGCGACAAGGCTCC-1_contig_1</td>\n",
       "      <td>ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-69*01</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1535695</th>\n",
       "      <td>TTCGGTCTCAACTCTT-1_contig_1</td>\n",
       "      <td>TGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-38-2*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>361113</th>\n",
       "      <td>CATGCCTGTCTTTCAT-1_contig_2</td>\n",
       "      <td>AAATTCAGGTTCCAGCTCACATGGGAAATACTTTCTGAGAGTCCTG...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-61*01</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>748949</th>\n",
       "      <td>CACATAGAGTGCGATG-1_contig_1</td>\n",
       "      <td>GGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-59*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>839076</th>\n",
       "      <td>GACGGCTTCTTCGAGA-1_contig_2</td>\n",
       "      <td>AGCTCTGGGAGAAGAGCCCCAGCCCCAGAATTCCCAGGAGTTTCCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-11*05</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'V', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1000 rows × 200 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence_id_heavy  \\\n",
       "1537568  AACTCAGAGTTGTAGA-1_contig_1   \n",
       "1390188  TGCCAAACAATCACAC-1_contig_1   \n",
       "413004   AGTCTTTCATTGGGCC-1_contig_1   \n",
       "260850   CATCCACAGTGAAGTT-1_contig_1   \n",
       "981594   GACGGCTTCTTCTGGC-1_contig_2   \n",
       "...                              ...   \n",
       "1175461  AGAGCGACAAGGCTCC-1_contig_1   \n",
       "1535695  TTCGGTCTCAACTCTT-1_contig_1   \n",
       "361113   CATGCCTGTCTTTCAT-1_contig_2   \n",
       "748949   CACATAGAGTGCGATG-1_contig_1   \n",
       "839076   GACGGCTTCTTCGAGA-1_contig_2   \n",
       "\n",
       "                                            sequence_heavy locus_heavy  \\\n",
       "1537568  ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...           H   \n",
       "1390188  TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...           H   \n",
       "413004   ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...           H   \n",
       "260850   GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...           H   \n",
       "981594   CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...           H   \n",
       "...                                                    ...         ...   \n",
       "1175461  ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...           H   \n",
       "1535695  TGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGC...           H   \n",
       "361113   AAATTCAGGTTCCAGCTCACATGGGAAATACTTTCTGAGAGTCCTG...           H   \n",
       "748949   GGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGA...           H   \n",
       "839076   AGCTCTGGGAGAAGAGCCCCAGCCCCAGAATTCCCAGGAGTTTCCA...           H   \n",
       "\n",
       "        stop_codon_heavy vj_in_frame_heavy v_frameshift_heavy  \\\n",
       "1537568                F                 T                  F   \n",
       "1390188                F                 T                  F   \n",
       "413004                 F                 T                  F   \n",
       "260850                 F                 T                  F   \n",
       "981594                 F                 T                  F   \n",
       "...                  ...               ...                ...   \n",
       "1175461                F                 T                  F   \n",
       "1535695                F                 T                  F   \n",
       "361113                 F                 T                  F   \n",
       "748949                 F                 T                  F   \n",
       "839076                 F                 T                  F   \n",
       "\n",
       "        productive_heavy rev_comp_heavy complete_vdj_heavy   v_call_heavy  \\\n",
       "1537568                T              F                  T    IGHV1-69*01   \n",
       "1390188                T              F                  T  IGHV4-38-2*02   \n",
       "413004                 T              F                  T    IGHV4-59*01   \n",
       "260850                 T              F                  T    IGHV3-21*01   \n",
       "981594                 T              F                  T    IGHV3-30*04   \n",
       "...                  ...            ...                ...            ...   \n",
       "1175461                T              F                  T    IGHV1-69*01   \n",
       "1535695                T              F                  T  IGHV4-38-2*01   \n",
       "361113                 T              F                  T    IGHV4-61*01   \n",
       "748949                 T              F                  T    IGHV4-59*01   \n",
       "839076                 T              F                  T    IGHV3-11*05   \n",
       "\n",
       "         ... np1_length_light np2_light np2_length_light  \\\n",
       "1537568  ...              4.0       NaN              NaN   \n",
       "1390188  ...              2.0       NaN              NaN   \n",
       "413004   ...              0.0       NaN              NaN   \n",
       "260850   ...              2.0       NaN              NaN   \n",
       "981594   ...              0.0       NaN              NaN   \n",
       "...      ...              ...       ...              ...   \n",
       "1175461  ...              1.0       NaN              NaN   \n",
       "1535695  ...              0.0       NaN              NaN   \n",
       "361113   ...              2.0       NaN              NaN   \n",
       "748949   ...              0.0       NaN              NaN   \n",
       "839076   ...              0.0       NaN              NaN   \n",
       "\n",
       "                                            c_region_light Isotype_light  \\\n",
       "1537568  GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "1390188  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "413004   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "260850   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "981594   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "...                                                    ...           ...   \n",
       "1175461  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "1535695  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "361113   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "748949   GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "839076   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "\n",
       "        Redundancy_light                             ANARCI_numbering_light  \\\n",
       "1537568              1.0  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...   \n",
       "1390188              1.0  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...   \n",
       "413004               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "260850               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "981594               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "...                  ...                                                ...   \n",
       "1175461              1.0  {'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "1535695              1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "361113               1.0  {'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "748949               1.0  {'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...   \n",
       "839076               1.0  {'fwk1': {'1 ': 'D', '2 ': 'V', '3 ': 'V', '4 ...   \n",
       "\n",
       "         ANARCI_status_light  integer_encoded_letters_392.0  \\\n",
       "1537568                |||||                              0   \n",
       "1390188                |||||                              0   \n",
       "413004                 |||||                              0   \n",
       "260850                 |||||                              0   \n",
       "981594                 |||||                              0   \n",
       "...                      ...                            ...   \n",
       "1175461                |||||                              0   \n",
       "1535695                |||||                              0   \n",
       "361113                 |||||                              0   \n",
       "748949                 |||||                              0   \n",
       "839076                 |||||                              0   \n",
       "\n",
       "         integer_encoded_letters_719.0  \n",
       "1537568                              0  \n",
       "1390188                              0  \n",
       "413004                               0  \n",
       "260850                               0  \n",
       "981594                               0  \n",
       "...                                ...  \n",
       "1175461                              0  \n",
       "1535695                              0  \n",
       "361113                               0  \n",
       "748949                               0  \n",
       "839076                               0  \n",
       "\n",
       "[1000 rows x 200 columns]"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#use get dummies()\n",
    "df_dummies = pd.get_dummies(small_df, prefix = ['integer_encoded_letters'], columns = ['integer_encoded_letters'], drop_first = True)\n",
    "df_dummies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "id": "023f924e",
   "metadata": {},
   "outputs": [],
   "source": [
    "#functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "id": "59b8ab1f",
   "metadata": {},
   "outputs": [],
   "source": [
    "#can motify it when know which columns to use later\n",
    "def one_hot_encode_seq(df, column):\n",
    "    #Output a df with a specific columns that want to get dummies in\n",
    "    \n",
    "    #label_encode\n",
    "    le = LabelEncoder()\n",
    "    le.fit(df[column])\n",
    "    integer_encoded_letters_arry = le.transform(small_df[column])\n",
    "    \n",
    "    #append\n",
    "    integer_encoded_letters_series = pd.Series(integer_encoded_letters_arry)\n",
    "    df['integer_encoded_letters'] = integer_encoded_letters_series\n",
    "    \n",
    "    #one hot encode\n",
    "    df_dummies = pd.get_dummies(df, prefix = ['integer_encoded_letters'], columns = ['integer_encoded_letters'], drop_first = True)\n",
    "    return df_dummies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "id": "30f5140e",
   "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>sequence_id_heavy</th>\n",
       "      <th>sequence_heavy</th>\n",
       "      <th>locus_heavy</th>\n",
       "      <th>stop_codon_heavy</th>\n",
       "      <th>vj_in_frame_heavy</th>\n",
       "      <th>v_frameshift_heavy</th>\n",
       "      <th>productive_heavy</th>\n",
       "      <th>rev_comp_heavy</th>\n",
       "      <th>complete_vdj_heavy</th>\n",
       "      <th>v_call_heavy</th>\n",
       "      <th>...</th>\n",
       "      <th>np1_length_light</th>\n",
       "      <th>np2_light</th>\n",
       "      <th>np2_length_light</th>\n",
       "      <th>c_region_light</th>\n",
       "      <th>Isotype_light</th>\n",
       "      <th>Redundancy_light</th>\n",
       "      <th>ANARCI_numbering_light</th>\n",
       "      <th>ANARCI_status_light</th>\n",
       "      <th>integer_encoded_letters_392.0</th>\n",
       "      <th>integer_encoded_letters_719.0</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1537568</th>\n",
       "      <td>AACTCAGAGTTGTAGA-1_contig_1</td>\n",
       "      <td>ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-69*01</td>\n",
       "      <td>...</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1390188</th>\n",
       "      <td>TGCCAAACAATCACAC-1_contig_1</td>\n",
       "      <td>TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-38-2*02</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>413004</th>\n",
       "      <td>AGTCTTTCATTGGGCC-1_contig_1</td>\n",
       "      <td>ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-59*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>260850</th>\n",
       "      <td>CATCCACAGTGAAGTT-1_contig_1</td>\n",
       "      <td>GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-21*01</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>981594</th>\n",
       "      <td>GACGGCTTCTTCTGGC-1_contig_2</td>\n",
       "      <td>CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-30*04</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</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",
       "      <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",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1175461</th>\n",
       "      <td>AGAGCGACAAGGCTCC-1_contig_1</td>\n",
       "      <td>ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV1-69*01</td>\n",
       "      <td>...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1535695</th>\n",
       "      <td>TTCGGTCTCAACTCTT-1_contig_1</td>\n",
       "      <td>TGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGC...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-38-2*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>361113</th>\n",
       "      <td>CATGCCTGTCTTTCAT-1_contig_2</td>\n",
       "      <td>AAATTCAGGTTCCAGCTCACATGGGAAATACTTTCTGAGAGTCCTG...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-61*01</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>748949</th>\n",
       "      <td>CACATAGAGTGCGATG-1_contig_1</td>\n",
       "      <td>GGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV4-59*01</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>839076</th>\n",
       "      <td>GACGGCTTCTTCGAGA-1_contig_2</td>\n",
       "      <td>AGCTCTGGGAGAAGAGCCCCAGCCCCAGAATTCCCAGGAGTTTCCA...</td>\n",
       "      <td>H</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>F</td>\n",
       "      <td>T</td>\n",
       "      <td>IGHV3-11*05</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...</td>\n",
       "      <td>Bulk</td>\n",
       "      <td>1.0</td>\n",
       "      <td>{'fwk1': {'1 ': 'D', '2 ': 'V', '3 ': 'V', '4 ...</td>\n",
       "      <td>|||||</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1000 rows × 200 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence_id_heavy  \\\n",
       "1537568  AACTCAGAGTTGTAGA-1_contig_1   \n",
       "1390188  TGCCAAACAATCACAC-1_contig_1   \n",
       "413004   AGTCTTTCATTGGGCC-1_contig_1   \n",
       "260850   CATCCACAGTGAAGTT-1_contig_1   \n",
       "981594   GACGGCTTCTTCTGGC-1_contig_2   \n",
       "...                              ...   \n",
       "1175461  AGAGCGACAAGGCTCC-1_contig_1   \n",
       "1535695  TTCGGTCTCAACTCTT-1_contig_1   \n",
       "361113   CATGCCTGTCTTTCAT-1_contig_2   \n",
       "748949   CACATAGAGTGCGATG-1_contig_1   \n",
       "839076   GACGGCTTCTTCGAGA-1_contig_2   \n",
       "\n",
       "                                            sequence_heavy locus_heavy  \\\n",
       "1537568  ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...           H   \n",
       "1390188  TTTGGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGA...           H   \n",
       "413004   ACATGGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAAC...           H   \n",
       "260850   GAGAGAGGAGCCTTAGCCCTGGATTCCAAGGCCTATCCACTTGGTG...           H   \n",
       "981594   CGAGCCCAGCACTGGAAGTCGCCGGTGTTTCCATTCGGTGATCAGC...           H   \n",
       "...                                                    ...         ...   \n",
       "1175461  ATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCA...           H   \n",
       "1535695  TGGGGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGC...           H   \n",
       "361113   AAATTCAGGTTCCAGCTCACATGGGAAATACTTTCTGAGAGTCCTG...           H   \n",
       "748949   GGGAAATACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGA...           H   \n",
       "839076   AGCTCTGGGAGAAGAGCCCCAGCCCCAGAATTCCCAGGAGTTTCCA...           H   \n",
       "\n",
       "        stop_codon_heavy vj_in_frame_heavy v_frameshift_heavy  \\\n",
       "1537568                F                 T                  F   \n",
       "1390188                F                 T                  F   \n",
       "413004                 F                 T                  F   \n",
       "260850                 F                 T                  F   \n",
       "981594                 F                 T                  F   \n",
       "...                  ...               ...                ...   \n",
       "1175461                F                 T                  F   \n",
       "1535695                F                 T                  F   \n",
       "361113                 F                 T                  F   \n",
       "748949                 F                 T                  F   \n",
       "839076                 F                 T                  F   \n",
       "\n",
       "        productive_heavy rev_comp_heavy complete_vdj_heavy   v_call_heavy  \\\n",
       "1537568                T              F                  T    IGHV1-69*01   \n",
       "1390188                T              F                  T  IGHV4-38-2*02   \n",
       "413004                 T              F                  T    IGHV4-59*01   \n",
       "260850                 T              F                  T    IGHV3-21*01   \n",
       "981594                 T              F                  T    IGHV3-30*04   \n",
       "...                  ...            ...                ...            ...   \n",
       "1175461                T              F                  T    IGHV1-69*01   \n",
       "1535695                T              F                  T  IGHV4-38-2*01   \n",
       "361113                 T              F                  T    IGHV4-61*01   \n",
       "748949                 T              F                  T    IGHV4-59*01   \n",
       "839076                 T              F                  T    IGHV3-11*05   \n",
       "\n",
       "         ... np1_length_light np2_light np2_length_light  \\\n",
       "1537568  ...              4.0       NaN              NaN   \n",
       "1390188  ...              2.0       NaN              NaN   \n",
       "413004   ...              0.0       NaN              NaN   \n",
       "260850   ...              2.0       NaN              NaN   \n",
       "981594   ...              0.0       NaN              NaN   \n",
       "...      ...              ...       ...              ...   \n",
       "1175461  ...              1.0       NaN              NaN   \n",
       "1535695  ...              0.0       NaN              NaN   \n",
       "361113   ...              2.0       NaN              NaN   \n",
       "748949   ...              0.0       NaN              NaN   \n",
       "839076   ...              0.0       NaN              NaN   \n",
       "\n",
       "                                            c_region_light Isotype_light  \\\n",
       "1537568  GTCAGCCCAAGGCCAACCCCACTGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "1390188  GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "413004   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "260850   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "981594   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "...                                                    ...           ...   \n",
       "1175461  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "1535695  GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "361113   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "748949   GTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCGCCCTCCTC...          Bulk   \n",
       "839076   GAACTGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATGA...          Bulk   \n",
       "\n",
       "        Redundancy_light                             ANARCI_numbering_light  \\\n",
       "1537568              1.0  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'E', '4 ...   \n",
       "1390188              1.0  {'fwl1': {'1 ': 'S', '2 ': 'Y', '3 ': 'V', '4 ...   \n",
       "413004               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "260850               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "981594               1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "...                  ...                                                ...   \n",
       "1175461              1.0  {'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "1535695              1.0  {'fwk1': {'1 ': 'D', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "361113               1.0  {'fwk1': {'1 ': 'E', '2 ': 'I', '3 ': 'V', '4 ...   \n",
       "748949               1.0  {'fwl1': {'1 ': 'Q', '2 ': 'S', '3 ': 'V', '4 ...   \n",
       "839076               1.0  {'fwk1': {'1 ': 'D', '2 ': 'V', '3 ': 'V', '4 ...   \n",
       "\n",
       "         ANARCI_status_light  integer_encoded_letters_392.0  \\\n",
       "1537568                |||||                              0   \n",
       "1390188                |||||                              0   \n",
       "413004                 |||||                              0   \n",
       "260850                 |||||                              0   \n",
       "981594                 |||||                              0   \n",
       "...                      ...                            ...   \n",
       "1175461                |||||                              0   \n",
       "1535695                |||||                              0   \n",
       "361113                 |||||                              0   \n",
       "748949                 |||||                              0   \n",
       "839076                 |||||                              0   \n",
       "\n",
       "         integer_encoded_letters_719.0  \n",
       "1537568                              0  \n",
       "1390188                              0  \n",
       "413004                               0  \n",
       "260850                               0  \n",
       "981594                               0  \n",
       "...                                ...  \n",
       "1175461                              0  \n",
       "1535695                              0  \n",
       "361113                               0  \n",
       "748949                               0  \n",
       "839076                               0  \n",
       "\n",
       "[1000 rows x 200 columns]"
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "encode_df = one_hot_encode_seq(small_df, 'sequence_alignment_aa_heavy')\n",
    "encode_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "id": "f8602181",
   "metadata": {},
   "outputs": [],
   "source": [
    "alph = np.array(sorted('ACDEFGHIKLMNPQRSTVWY'))\n",
    "residue_info = pd.read_csv(\"residue_dict_copy.csv\", header = 0, index_col = 0)\n",
    "def physchemvh_gen(df, column):\n",
    "    res_counts = pd.DataFrame(index = alph)\n",
    "    df = df.set_index(column)\n",
    "    for i in df.index:\n",
    "        characters = pd.Series(list(i))\n",
    "        res_counts = pd.concat([res_counts, characters.value_counts()], axis = 1, ignore_index = False)\n",
    "    res_counts.fillna(0, inplace = True)\n",
    "    res_counts = res_counts.T\n",
    "    hydrophobicity = []    \n",
    "    for column in res_counts:\n",
    "        hydros = []\n",
    "        for index, row in res_counts.iterrows():\n",
    "            hydros.append(row[column]*residue_info.loc[column, 'Hydropathy Score'])\n",
    "        hydrophobicity.append(hydros)\n",
    "    hydrophobicity = pd.DataFrame(hydrophobicity).T\n",
    "    hydrophobicity['ave'] = hydrophobicity.sum(axis = 1)/115\n",
    "    res_counts['Hydro'] = res_counts['A'] +  res_counts['I'] +  res_counts['L']+  res_counts['F']+  res_counts['V']\n",
    "    res_counts['Amph'] = res_counts['W'] +  res_counts['Y']+  res_counts['M']\n",
    "    res_counts['Polar'] = res_counts['Q'] +  res_counts['N'] + res_counts['S'] +  res_counts['T'] +  res_counts['C']+  res_counts['M']\n",
    "    res_counts['Charged'] =  res_counts['R'] +  res_counts['K'] + res_counts['D'] +  res_counts['E'] +  res_counts['H']\n",
    "    res_counts.reset_index(drop = True, inplace = True)\n",
    "    physchemvh = pd.concat([res_counts, hydrophobicity['ave']], axis = 1, ignore_index = False)\n",
    "    return physchemvh"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "id": "f10bd93a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# small_df_temp = small_df.set_index('sequence_alignment_aa_heavy')\n",
    "# small_df_temp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "id": "0c70380d",
   "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",
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       "    .dataframe thead th {\n",
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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>A</th>\n",
       "      <th>C</th>\n",
       "      <th>D</th>\n",
       "      <th>E</th>\n",
       "      <th>F</th>\n",
       "      <th>G</th>\n",
       "      <th>H</th>\n",
       "      <th>I</th>\n",
       "      <th>K</th>\n",
       "      <th>L</th>\n",
       "      <th>...</th>\n",
       "      <th>S</th>\n",
       "      <th>T</th>\n",
       "      <th>V</th>\n",
       "      <th>W</th>\n",
       "      <th>Y</th>\n",
       "      <th>Hydro</th>\n",
       "      <th>Amph</th>\n",
       "      <th>Polar</th>\n",
       "      <th>Charged</th>\n",
       "      <th>ave</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>10.0</td>\n",
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       "      <td>6.0</td>\n",
       "      <td>...</td>\n",
       "      <td>15.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>-0.286087</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>5.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>...</td>\n",
       "      <td>19.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>-0.245217</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>...</td>\n",
       "      <td>20.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>-0.300000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>8.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>...</td>\n",
       "      <td>20.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>-0.266087</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>9.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>...</td>\n",
       "      <td>17.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>-0.281739</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <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",
       "      <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>995</th>\n",
       "      <td>11.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>...</td>\n",
       "      <td>15.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>-0.153913</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>996</th>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>...</td>\n",
       "      <td>18.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>-0.234783</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>997</th>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>...</td>\n",
       "      <td>20.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>-0.116522</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>998</th>\n",
       "      <td>6.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>...</td>\n",
       "      <td>20.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>43.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>-0.232174</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>999</th>\n",
       "      <td>7.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>...</td>\n",
       "      <td>14.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>-0.240000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1000 rows × 25 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        A    C    D    E    F     G    H    I    K     L  ...     S     T  \\\n",
       "0    10.0  2.0  4.0  5.0  3.0  15.0  1.0  5.0  5.0   6.0  ...  15.0   9.0   \n",
       "1     5.0  2.0  5.0  4.0  2.0  12.0  1.0  5.0  5.0   9.0  ...  19.0  10.0   \n",
       "2     4.0  2.0  5.0  3.0  1.0  12.0  1.0  5.0  5.0   9.0  ...  20.0  11.0   \n",
       "3     8.0  2.0  6.0  4.0  3.0  12.0  0.0  3.0  5.0   8.0  ...  20.0   9.0   \n",
       "4     9.0  2.0  6.0  3.0  3.0  14.0  1.0  2.0  4.0   9.0  ...  17.0   7.0   \n",
       "..    ...  ...  ...  ...  ...   ...  ...  ...  ...   ...  ...   ...   ...   \n",
       "995  11.0  2.0  4.0  5.0  4.0  14.0  0.0  6.0  6.0   4.0  ...  15.0   9.0   \n",
       "996   6.0  2.0  4.0  3.0  3.0  12.0  4.0  6.0  4.0  10.0  ...  18.0   8.0   \n",
       "997   6.0  2.0  3.0  3.0  2.0  13.0  0.0  5.0  5.0  10.0  ...  20.0  10.0   \n",
       "998   6.0  2.0  4.0  4.0  2.0  14.0  0.0  8.0  5.0   9.0  ...  20.0  11.0   \n",
       "999   7.0  2.0  6.0  4.0  3.0  13.0  2.0  3.0  2.0  11.0  ...  14.0   9.0   \n",
       "\n",
       "        V    W     Y  Hydro  Amph  Polar  Charged       ave  \n",
       "0    10.0  3.0   6.0   34.0  11.0   40.0     19.0 -0.286087  \n",
       "1    11.0  5.0   8.0   32.0  13.0   40.0     18.0 -0.245217  \n",
       "2    10.0  4.0  11.0   29.0  16.0   43.0     17.0 -0.300000  \n",
       "3    11.0  4.0  11.0   33.0  18.0   41.0     21.0 -0.266087  \n",
       "4    12.0  4.0   9.0   35.0  15.0   38.0     21.0 -0.281739  \n",
       "..    ...  ...   ...    ...   ...    ...      ...       ...  \n",
       "995  10.0  3.0   6.0   35.0  12.0   38.0     19.0 -0.153913  \n",
       "996   8.0  4.0   8.0   33.0  13.0   40.0     18.0 -0.234783  \n",
       "997  11.0  4.0   9.0   34.0  13.0   41.0     15.0 -0.116522  \n",
       "998   9.0  4.0  12.0   34.0  17.0   43.0     18.0 -0.232174  \n",
       "999   9.0  3.0   7.0   33.0  12.0   37.0     20.0 -0.240000  \n",
       "\n",
       "[1000 rows x 25 columns]"
      ]
     },
     "execution_count": 72,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "physchemvh_gen(small_df, 'sequence_alignment_aa_heavy')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bc67d90c-49ac-42db-bbf3-0154b549a7c3",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a3874437-af4a-42ae-be09-0aa485cca558",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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