generate_dms_mutants_V2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "5a1c19ab-8bfe-41c4-9cba-997502fcdd72",
   "metadata": {},
   "source": [
    "# Notebook to generate dataframes of DMS mutants"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "645b8cc8-271b-4db8-b8ba-713ceea64a46",
   "metadata": {},
   "source": [
    "## Import libraries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "244fa757-02f9-4ea6-adb2-f57cfc01b6a5",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cd4a00c2-da22-493a-9f04-58c26f456d71",
   "metadata": {},
   "source": [
    "## Functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "6347b531-693e-4072-a793-f3aaa93113f9",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_nt_seq(wt_seq, mut_dic):\n",
    "    wt_list_codons = [wt_seq[i:i+3] for i in range(0, len(wt_seq), 3)] # Converting WT nucleotide sequence to list of codons\n",
    "    seq_l = [mut_dic[a] if a in mut_dic.keys() else wtcodon for a, wtcodon in enumerate(wt_list_codons)]\n",
    "    return ''.join(seq_l)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "6ca862cb-3e83-4c92-808e-9a9a8012ef3d",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "def get_alt_codons(nt_seq, wt_seq):\n",
    "    list_alt_pos = []\n",
    "    list_alt_cod = []\n",
    "    wt_list_codons = [wt_seq[i:i+3] for i in range(0, len(wt_seq), 3)] # Converting WT nucleotide sequence to list of codons\n",
    "    seq_list_codons = [nt_seq[i:i+3] for i in range(0, len(nt_seq), 3)] # Converting nucleotide sequence of variant to list of codons\n",
    "    for i, c in enumerate(seq_list_codons):\n",
    "        if c != wt_list_codons[i]:\n",
    "            list_alt_pos.append(i)\n",
    "            list_alt_cod.append(c)\n",
    "    \n",
    "    return list(range(1,len(list_alt_pos)+1)), list_alt_pos, list_alt_cod"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c566e6c1-47bf-40a4-a7fa-4dd167cd16f2",
   "metadata": {},
   "source": [
    "## Specify locus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "2f2a5de5-af8a-4c95-a227-aae88b087353",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "locus = 'FKS2-HS2'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d69ace40-5527-4e62-af3f-b90113daedd5",
   "metadata": {},
   "source": [
    "## Specify paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "2812be6c-9e0a-4c63-9a81-72dadd073a1d",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "codon_table_path = 'data/general_use/ScerevisiaeTAXID559292_Cocoputs_codon_table.csv'\n",
    "wtseqs_path = 'data/general_use/wtseqs.csv'\n",
    "ortho_path = f'orthologs/{locus}_ortholog_nt.csv'\n",
    "outpath_f = f'data/{locus}/{locus}_var_df.csv'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d892e88-b2b3-4a73-99a1-ba211882b25f",
   "metadata": {},
   "source": [
    "## Get WT and possible mutations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "5761f45c-3857-4a2d-87b1-18be2058afbc",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'tttttagttttatctttgagagatcca'"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "wtseqs = pd.read_csv(wtseqs_path, header=0)\n",
    "wtseq = wtseqs.loc[wtseqs.locus == locus, 'nt_seq'].values[0]\n",
    "wtseq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "e1e6b9e6-01f1-4390-8bd1-d6f533865582",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>codon</th>\n",
       "      <th>aminoacid</th>\n",
       "      <th>freq</th>\n",
       "      <th>number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ttt</td>\n",
       "      <td>F</td>\n",
       "      <td>26.26</td>\n",
       "      <td>76999</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ttc</td>\n",
       "      <td>F</td>\n",
       "      <td>17.89</td>\n",
       "      <td>52459</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>tta</td>\n",
       "      <td>L</td>\n",
       "      <td>26.31</td>\n",
       "      <td>77131</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "  codon aminoacid   freq  number\n",
       "0   ttt         F  26.26   76999\n",
       "1   ttc         F  17.89   52459\n",
       "2   tta         L  26.31   77131"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "codon_table = pd.read_csv(codon_table_path, header=0)\n",
    "codon_table['codon'] = codon_table['codon'].str.lower()\n",
    "codon_table.head(3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "ddce0762-9863-4304-8442-60f208d4f65c",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'ttt': 'F', 'ttc': 'F', 'tta': 'L', 'ttg': 'L', 'ctt': 'L', 'ctc': 'L', 'cta': 'L', 'ctg': 'L', 'att': 'I', 'atc': 'I', 'ata': 'I', 'atg': 'M', 'gtt': 'V', 'gtc': 'V', 'gta': 'V', 'gtg': 'V', 'tct': 'S', 'tcc': 'S', 'tca': 'S', 'tcg': 'S', 'cct': 'P', 'ccc': 'P', 'cca': 'P', 'ccg': 'P', 'act': 'T', 'acc': 'T', 'aca': 'T', 'acg': 'T', 'gct': 'A', 'gcc': 'A', 'gca': 'A', 'gcg': 'A', 'tat': 'Y', 'tac': 'Y', 'taa': '*', 'tag': '*', 'cat': 'H', 'cac': 'H', 'caa': 'Q', 'cag': 'Q', 'aat': 'N', 'aac': 'N', 'aaa': 'K', 'aag': 'K', 'gat': 'D', 'gac': 'D', 'gaa': 'E', 'gag': 'E', 'tgt': 'C', 'tgc': 'C', 'tga': '*', 'tgg': 'W', 'cgt': 'R', 'cgc': 'R', 'cga': 'R', 'cgg': 'R', 'agt': 'S', 'agc': 'S', 'aga': 'R', 'agg': 'R', 'ggt': 'G', 'ggc': 'G', 'gga': 'G', 'ggg': 'G'}\n"
     ]
    }
   ],
   "source": [
    "# Converting to dictionary\n",
    "codon_dic = dict(zip(codon_table['codon'], codon_table['aminoacid']))\n",
    "print(codon_dic)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "503ca887-e36d-456e-a473-9e40e5e3bd40",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "32"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nnk = [x for x in codon_dic.keys() if x[2] in ['g', 't']]\n",
    "len(nnk)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4886fb93-1ad8-4fef-ab3d-2bf490182e5d",
   "metadata": {},
   "source": [
    "## Generate single mutants"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "29b229e3-2eae-45fd-a888-b5dfec56b515",
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   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "      <th>seq_type</th>\n",
       "      <th>mutated_codon</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>single</td>\n",
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       "      <th>3</th>\n",
       "      <td>3</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
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       "      <td>single</td>\n",
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       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>5</td>\n",
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       "      <td>single</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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      ],
      "text/plain": [
       "   aa_pos                                         alt_codons seq_type  \\\n",
       "0       0  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "1       1  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "2       2  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   single   \n",
       "3       3  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "4       4  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "5       5  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "6       6  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "7       7  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   single   \n",
       "\n",
       "   mutated_codon  \n",
       "0              1  \n",
       "1              1  \n",
       "2              1  \n",
       "3              1  \n",
       "4              1  \n",
       "5              1  \n",
       "6              1  \n",
       "7              1  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rows_l = []\n",
    "\n",
    "for i in range(0,len(wtseq),3):\n",
    "    list_var = [x for x in nnk if x != wtseq[i:i+3]]\n",
    "    #print(len(list_var))\n",
    "    rows_l.append([\n",
    "              i//3, # 0-based position (aa)\n",
    "              list_var # list of possible NNK codons other than WT\n",
    "                  ])\n",
    "\n",
    "singles_compact_df = pd.DataFrame(rows_l, columns = ['aa_pos', 'alt_codons'])\n",
    "singles_compact_df['seq_type'] = 'single'\n",
    "singles_compact_df['mutated_codon'] = 1\n",
    "singles_compact_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "e57862b0-0fec-42b7-aa44-81a68eb73abd",
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   "outputs": [
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       "      <th></th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "      <th>seq_type</th>\n",
       "      <th>mutated_codon</th>\n",
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       "  </thead>\n",
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       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ttt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ttg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ctt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ctg</td>\n",
       "      <td>single</td>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>att</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
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       "      <th>...</th>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>cgg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>agt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>agg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>ggt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>251 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    aa_pos alt_codons seq_type  mutated_codon\n",
       "0        0        ttt   single              1\n",
       "0        0        ttg   single              1\n",
       "0        0        ctt   single              1\n",
       "0        0        ctg   single              1\n",
       "0        0        att   single              1\n",
       "..     ...        ...      ...            ...\n",
       "7        7        cgg   single              1\n",
       "7        7        agt   single              1\n",
       "7        7        agg   single              1\n",
       "7        7        ggt   single              1\n",
       "7        7        ggg   single              1\n",
       "\n",
       "[251 rows x 4 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "singles_df = singles_compact_df.explode('alt_codons')\n",
    "singles_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "422e6263-bfca-4351-bf2c-2309d8c2d756",
   "metadata": {},
   "outputs": [
    {
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       "      <th>alt_codons</th>\n",
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       "      <th>mutated_codon</th>\n",
       "      <th>mutations</th>\n",
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       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ttt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{0: 'ttt'}</td>\n",
       "    </tr>\n",
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       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ttg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{0: 'ttg'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ctt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{0: 'ctt'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ctg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{0: 'ctg'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>att</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{0: 'att'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>cgg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{7: 'cgg'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>agt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{7: 'agt'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>agg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{7: 'agg'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>ggt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{7: 'ggt'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>{7: 'ggg'}</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>251 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    aa_pos alt_codons seq_type  mutated_codon   mutations\n",
       "0        0        ttt   single              1  {0: 'ttt'}\n",
       "0        0        ttg   single              1  {0: 'ttg'}\n",
       "0        0        ctt   single              1  {0: 'ctt'}\n",
       "0        0        ctg   single              1  {0: 'ctg'}\n",
       "0        0        att   single              1  {0: 'att'}\n",
       "..     ...        ...      ...            ...         ...\n",
       "7        7        cgg   single              1  {7: 'cgg'}\n",
       "7        7        agt   single              1  {7: 'agt'}\n",
       "7        7        agg   single              1  {7: 'agg'}\n",
       "7        7        ggt   single              1  {7: 'ggt'}\n",
       "7        7        ggg   single              1  {7: 'ggg'}\n",
       "\n",
       "[251 rows x 5 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "singles_df['mutations'] = singles_df.apply(lambda row: {row[f'aa_pos']: row[f'alt_codons']}, axis=1)\n",
    "singles_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "02dd892f-a4ce-4509-b2bd-3ed9c2cfd453",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "      <th>seq_type</th>\n",
       "      <th>mutated_codon</th>\n",
       "      <th>nt_seq</th>\n",
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       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>ttt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>ttttgggtgagacgttatacactc</td>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
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       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>cgg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>gattgggtgagacgttatacacgg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>agt</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>gattgggtgagacgttatacaagt</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
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       "      <th>7</th>\n",
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       "      <td>1</td>\n",
       "      <td>gattgggtgagacgttatacaggt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>single</td>\n",
       "      <td>1</td>\n",
       "      <td>gattgggtgagacgttatacaggg</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>251 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    aa_pos alt_codons seq_type  mutated_codon                    nt_seq\n",
       "0        0        ttt   single              1  ttttgggtgagacgttatacactc\n",
       "0        0        ttg   single              1  ttgtgggtgagacgttatacactc\n",
       "0        0        ctt   single              1  ctttgggtgagacgttatacactc\n",
       "0        0        ctg   single              1  ctgtgggtgagacgttatacactc\n",
       "0        0        att   single              1  atttgggtgagacgttatacactc\n",
       "..     ...        ...      ...            ...                       ...\n",
       "7        7        cgg   single              1  gattgggtgagacgttatacacgg\n",
       "7        7        agt   single              1  gattgggtgagacgttatacaagt\n",
       "7        7        agg   single              1  gattgggtgagacgttatacaagg\n",
       "7        7        ggt   single              1  gattgggtgagacgttatacaggt\n",
       "7        7        ggg   single              1  gattgggtgagacgttatacaggg\n",
       "\n",
       "[251 rows x 5 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "singles_df['nt_seq'] = singles_df.mutations.apply(lambda x: get_nt_seq(wtseq, x))\n",
    "singles_df.drop(columns='mutations', inplace=True)\n",
    "singles_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "48669775-ceeb-4a40-952d-22bd5d583820",
   "metadata": {},
   "source": [
    "## Generate double mutants"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "a37f83ec-9181-4dc4-8356-36d0e428e9f9",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[(0, 1), (0, 2), (0, 3), (0, 4), (0, 5), (0, 6), (0, 7), (1, 2), (1, 3), (1, 4), (1, 5), (1, 6), (1, 7), (2, 3), (2, 4), (2, 5), (2, 6), (2, 7), (3, 4), (3, 5), (3, 6), (3, 7), (4, 5), (4, 6), (4, 7), (5, 6), (5, 7), (6, 7)]\n"
     ]
    }
   ],
   "source": [
    "# First we generate a list of possible combinations (i, j) where i is the position of the first mutated aminoacid and j the position of the second one\n",
    "import itertools\n",
    "pos = range(0,len(wtseq)//3)\n",
    "combinations = list(itertools.combinations(pos, 2))\n",
    "print(combinations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "6a31c13d-e9ad-4678-ac08-70244f37cf86",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>combination</th>\n",
       "      <th>mutated_codon</th>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>(0, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>(0, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>(0, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>(0, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>(0, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>(1, 2)</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>(1, 2)</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
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       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>16</th>\n",
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       "      <td>1</td>\n",
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       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>(1, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
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       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>(1, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>(1, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
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       "    <tr>\n",
       "      <th>24</th>\n",
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       "      <th>26</th>\n",
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       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>(2, 3)</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>(2, 4)</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>(2, 4)</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>(2, 5)</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>(2, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>(2, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>(2, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>(2, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>(2, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>(3, 4)</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>(3, 4)</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>(3, 5)</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>(3, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>(3, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>(3, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>(3, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>(3, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>(4, 5)</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>(4, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>(4, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>(4, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>(4, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>(4, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>(5, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>(5, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>(5, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>(5, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   combination  mutated_codon  aa_pos  \\\n",
       "0       (0, 1)              1       0   \n",
       "1       (0, 1)              2       1   \n",
       "2       (0, 2)              1       0   \n",
       "3       (0, 2)              2       2   \n",
       "4       (0, 3)              1       0   \n",
       "5       (0, 3)              2       3   \n",
       "6       (0, 4)              1       0   \n",
       "7       (0, 4)              2       4   \n",
       "8       (0, 5)              1       0   \n",
       "9       (0, 5)              2       5   \n",
       "10      (0, 6)              1       0   \n",
       "11      (0, 6)              2       6   \n",
       "12      (0, 7)              1       0   \n",
       "13      (0, 7)              2       7   \n",
       "14      (1, 2)              1       1   \n",
       "15      (1, 2)              2       2   \n",
       "16      (1, 3)              1       1   \n",
       "17      (1, 3)              2       3   \n",
       "18      (1, 4)              1       1   \n",
       "19      (1, 4)              2       4   \n",
       "20      (1, 5)              1       1   \n",
       "21      (1, 5)              2       5   \n",
       "22      (1, 6)              1       1   \n",
       "23      (1, 6)              2       6   \n",
       "24      (1, 7)              1       1   \n",
       "25      (1, 7)              2       7   \n",
       "26      (2, 3)              1       2   \n",
       "27      (2, 3)              2       3   \n",
       "28      (2, 4)              1       2   \n",
       "29      (2, 4)              2       4   \n",
       "30      (2, 5)              1       2   \n",
       "31      (2, 5)              2       5   \n",
       "32      (2, 6)              1       2   \n",
       "33      (2, 6)              2       6   \n",
       "34      (2, 7)              1       2   \n",
       "35      (2, 7)              2       7   \n",
       "36      (3, 4)              1       3   \n",
       "37      (3, 4)              2       4   \n",
       "38      (3, 5)              1       3   \n",
       "39      (3, 5)              2       5   \n",
       "40      (3, 6)              1       3   \n",
       "41      (3, 6)              2       6   \n",
       "42      (3, 7)              1       3   \n",
       "43      (3, 7)              2       7   \n",
       "44      (4, 5)              1       4   \n",
       "45      (4, 5)              2       5   \n",
       "46      (4, 6)              1       4   \n",
       "47      (4, 6)              2       6   \n",
       "48      (4, 7)              1       4   \n",
       "49      (4, 7)              2       7   \n",
       "50      (5, 6)              1       5   \n",
       "51      (5, 6)              2       6   \n",
       "52      (5, 7)              1       5   \n",
       "53      (5, 7)              2       7   \n",
       "54      (6, 7)              1       6   \n",
       "55      (6, 7)              2       7   \n",
       "\n",
       "                                           alt_codons seq_type  \n",
       "0   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "1   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "2   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "3   [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "4   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "5   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "6   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "7   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "8   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "9   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "10  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "11  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "12  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "13  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "14  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "15  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "16  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "17  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "18  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "19  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "20  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "21  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "22  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "23  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "24  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "25  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "26  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "27  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "28  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "29  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "30  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "31  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "32  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "33  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "34  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   double  \n",
       "35  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "36  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "37  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "38  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "39  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "40  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "41  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "42  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "43  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "44  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "45  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "46  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "47  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "48  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "49  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "50  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "51  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "52  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "53  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "54  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  \n",
       "55  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   double  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rows_l = []\n",
    "\n",
    "for c in combinations:\n",
    "    for l in range(0,len(c)):\n",
    "        rows_l.append([\n",
    "                       c, # Combination\n",
    "                       l+1, # Mutated codon\n",
    "                       c[l], # 0-based position (aa)\n",
    "                       singles_compact_df.loc[singles_compact_df.aa_pos == c[l], 'alt_codons'].values[0], # list of possible NNK codons other than WT\n",
    "                      ])\n",
    "\n",
    "doubles_compact_df = pd.DataFrame(rows_l, columns = ['combination', 'mutated_codon', 'aa_pos', 'alt_codons'])\n",
    "doubles_compact_df['seq_type'] = 'double'\n",
    "doubles_compact_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "7c0875a7-00e5-4065-909e-da6a06051724",
   "metadata": {
    "tags": []
   },
   "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>seq_type</th>\n",
       "      <th>combination</th>\n",
       "      <th>aa_pos1</th>\n",
       "      <th>aa_pos2</th>\n",
       "      <th>alt_codons1</th>\n",
       "      <th>alt_codons2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 2)</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 3)</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 4)</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 5)</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 6)</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 7)</td>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 2)</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 3)</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 4)</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 5)</td>\n",
       "      <td>1</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 6)</td>\n",
       "      <td>1</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>double</td>\n",
       "      <td>(1, 7)</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>double</td>\n",
       "      <td>(2, 3)</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>double</td>\n",
       "      <td>(2, 4)</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>double</td>\n",
       "      <td>(2, 5)</td>\n",
       "      <td>2</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>double</td>\n",
       "      <td>(2, 6)</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>double</td>\n",
       "      <td>(2, 7)</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>double</td>\n",
       "      <td>(3, 4)</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>double</td>\n",
       "      <td>(3, 5)</td>\n",
       "      <td>3</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>double</td>\n",
       "      <td>(3, 6)</td>\n",
       "      <td>3</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>double</td>\n",
       "      <td>(3, 7)</td>\n",
       "      <td>3</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>double</td>\n",
       "      <td>(4, 5)</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>double</td>\n",
       "      <td>(4, 6)</td>\n",
       "      <td>4</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>double</td>\n",
       "      <td>(4, 7)</td>\n",
       "      <td>4</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>double</td>\n",
       "      <td>(5, 6)</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>double</td>\n",
       "      <td>(5, 7)</td>\n",
       "      <td>5</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "      <td>[ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   seq_type combination  aa_pos1  aa_pos2  \\\n",
       "0    double      (0, 1)        0        1   \n",
       "1    double      (0, 2)        0        2   \n",
       "2    double      (0, 3)        0        3   \n",
       "3    double      (0, 4)        0        4   \n",
       "4    double      (0, 5)        0        5   \n",
       "5    double      (0, 6)        0        6   \n",
       "6    double      (0, 7)        0        7   \n",
       "7    double      (1, 2)        1        2   \n",
       "8    double      (1, 3)        1        3   \n",
       "9    double      (1, 4)        1        4   \n",
       "10   double      (1, 5)        1        5   \n",
       "11   double      (1, 6)        1        6   \n",
       "12   double      (1, 7)        1        7   \n",
       "13   double      (2, 3)        2        3   \n",
       "14   double      (2, 4)        2        4   \n",
       "15   double      (2, 5)        2        5   \n",
       "16   double      (2, 6)        2        6   \n",
       "17   double      (2, 7)        2        7   \n",
       "18   double      (3, 4)        3        4   \n",
       "19   double      (3, 5)        3        5   \n",
       "20   double      (3, 6)        3        6   \n",
       "21   double      (3, 7)        3        7   \n",
       "22   double      (4, 5)        4        5   \n",
       "23   double      (4, 6)        4        6   \n",
       "24   double      (4, 7)        4        7   \n",
       "25   double      (5, 6)        5        6   \n",
       "26   double      (5, 7)        5        7   \n",
       "27   double      (6, 7)        6        7   \n",
       "\n",
       "                                          alt_codons1  \\\n",
       "0   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "1   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "2   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "3   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "4   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "5   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "6   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "7   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "8   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "9   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "10  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "11  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "12  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "13  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   \n",
       "14  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   \n",
       "15  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   \n",
       "16  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   \n",
       "17  [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...   \n",
       "18  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "19  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "20  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "21  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "22  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "23  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "24  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "25  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "26  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "27  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...   \n",
       "\n",
       "                                          alt_codons2  \n",
       "0   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "1   [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...  \n",
       "2   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "3   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "4   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "5   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "6   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "7   [ttt, ttg, ctt, ctg, att, atg, gtt, tct, tcg, ...  \n",
       "8   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "9   [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "10  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "11  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "12  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "13  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "14  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "15  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "16  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "17  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "18  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "19  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "20  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "21  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "22  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "23  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "24  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "25  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "26  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  \n",
       "27  [ttt, ttg, ctt, ctg, att, atg, gtt, gtg, tct, ...  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Dataframe is pivoted only to be able to use pd.explode(), then later on melted to go back to long format\n",
    "doubles_piv = doubles_compact_df.pivot_table(index = ['seq_type', 'combination'], columns = 'mutated_codon', values = ['aa_pos', 'alt_codons'], aggfunc = 'first').reset_index()\n",
    "doubles_piv.columns = [x[0] for x in doubles_piv.columns[:-4]] + [f\"{x[0]}{x[1]}\" for x in doubles_piv.columns[-4:]]\n",
    "doubles_piv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "738fb46e-6bbc-4a98-bd42-e25c660292da",
   "metadata": {
    "tags": []
   },
   "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>seq_type</th>\n",
       "      <th>combination</th>\n",
       "      <th>aa_pos1</th>\n",
       "      <th>aa_pos2</th>\n",
       "      <th>alt_codons1</th>\n",
       "      <th>alt_codons2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>ttt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>ttg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>ctt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>ctg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>att</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27557</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>cgg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27558</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>agt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27559</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>agg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27560</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>ggt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27561</th>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "      <td>ggg</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27562 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      seq_type combination  aa_pos1  aa_pos2 alt_codons1 alt_codons2\n",
       "0       double      (0, 1)        0        1         ttt         ttt\n",
       "1       double      (0, 1)        0        1         ttt         ttg\n",
       "2       double      (0, 1)        0        1         ttt         ctt\n",
       "3       double      (0, 1)        0        1         ttt         ctg\n",
       "4       double      (0, 1)        0        1         ttt         att\n",
       "...        ...         ...      ...      ...         ...         ...\n",
       "27557   double      (6, 7)        6        7         ggg         cgg\n",
       "27558   double      (6, 7)        6        7         ggg         agt\n",
       "27559   double      (6, 7)        6        7         ggg         agg\n",
       "27560   double      (6, 7)        6        7         ggg         ggt\n",
       "27561   double      (6, 7)        6        7         ggg         ggg\n",
       "\n",
       "[27562 rows x 6 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "doubles_exp1 = doubles_piv.explode('alt_codons1')\n",
    "doubles_exp2 = doubles_exp1.explode('alt_codons2')\n",
    "doubles_df = doubles_exp2.reset_index(drop=True)\n",
    "doubles_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "30afb189-e8ed-4f85-b93f-41a22508055e",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>seq_type</th>\n",
       "      <th>combination</th>\n",
       "      <th>aa_pos1</th>\n",
       "      <th>aa_pos2</th>\n",
       "      <th>alt_codons1</th>\n",
       "      <th>alt_codons2</th>\n",
       "      <th>mutations</th>\n",
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       "      <td>{0: 'ttt', 1: 'ttt'}</td>\n",
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       "      <td>{0: 'ttt', 1: 'att'}</td>\n",
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       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>atg</td>\n",
       "      <td>{0: 'ttt', 1: 'atg'}</td>\n",
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       "      <th>6</th>\n",
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       "      <td>ttt</td>\n",
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       "      <td>ttt</td>\n",
       "      <td>gtg</td>\n",
       "      <td>{0: 'ttt', 1: 'gtg'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>tct</td>\n",
       "      <td>{0: 'ttt', 1: 'tct'}</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>ttt</td>\n",
       "      <td>tcg</td>\n",
       "      <td>{0: 'ttt', 1: 'tcg'}</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  seq_type combination  aa_pos1  aa_pos2 alt_codons1 alt_codons2  \\\n",
       "0   double      (0, 1)        0        1         ttt         ttt   \n",
       "1   double      (0, 1)        0        1         ttt         ttg   \n",
       "2   double      (0, 1)        0        1         ttt         ctt   \n",
       "3   double      (0, 1)        0        1         ttt         ctg   \n",
       "4   double      (0, 1)        0        1         ttt         att   \n",
       "5   double      (0, 1)        0        1         ttt         atg   \n",
       "6   double      (0, 1)        0        1         ttt         gtt   \n",
       "7   double      (0, 1)        0        1         ttt         gtg   \n",
       "8   double      (0, 1)        0        1         ttt         tct   \n",
       "9   double      (0, 1)        0        1         ttt         tcg   \n",
       "\n",
       "              mutations  \n",
       "0  {0: 'ttt', 1: 'ttt'}  \n",
       "1  {0: 'ttt', 1: 'ttg'}  \n",
       "2  {0: 'ttt', 1: 'ctt'}  \n",
       "3  {0: 'ttt', 1: 'ctg'}  \n",
       "4  {0: 'ttt', 1: 'att'}  \n",
       "5  {0: 'ttt', 1: 'atg'}  \n",
       "6  {0: 'ttt', 1: 'gtt'}  \n",
       "7  {0: 'ttt', 1: 'gtg'}  \n",
       "8  {0: 'ttt', 1: 'tct'}  \n",
       "9  {0: 'ttt', 1: 'tcg'}  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "aa_pos_col = [x for x in doubles_df.columns if 'aa_pos' in x]\n",
    "aa_cod_col = [x for x in doubles_df.columns if 'alt_codons' in x]\n",
    "doubles_df['mutations'] = doubles_df.apply(lambda row: dict(zip(row[aa_pos_col].values,\n",
    "                                                                row[aa_cod_col].values\n",
    "                                                               )), axis=1)\n",
    "doubles_df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "cc6c86d8-e02e-4ed9-9291-c0d84a1c5a10",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>5</th>\n",
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       "      <td>ttt</td>\n",
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       "      <th>8</th>\n",
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       "      <td>0</td>\n",
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       "      <td>ttttctgtgagacgttatacactc</td>\n",
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       "      <th>9</th>\n",
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       "      <td>ttt</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  seq_type combination  aa_pos1  aa_pos2 alt_codons1 alt_codons2  \\\n",
       "0   double      (0, 1)        0        1         ttt         ttt   \n",
       "1   double      (0, 1)        0        1         ttt         ttg   \n",
       "2   double      (0, 1)        0        1         ttt         ctt   \n",
       "3   double      (0, 1)        0        1         ttt         ctg   \n",
       "4   double      (0, 1)        0        1         ttt         att   \n",
       "5   double      (0, 1)        0        1         ttt         atg   \n",
       "6   double      (0, 1)        0        1         ttt         gtt   \n",
       "7   double      (0, 1)        0        1         ttt         gtg   \n",
       "8   double      (0, 1)        0        1         ttt         tct   \n",
       "9   double      (0, 1)        0        1         ttt         tcg   \n",
       "\n",
       "                     nt_seq  \n",
       "0  ttttttgtgagacgttatacactc  \n",
       "1  tttttggtgagacgttatacactc  \n",
       "2  tttcttgtgagacgttatacactc  \n",
       "3  tttctggtgagacgttatacactc  \n",
       "4  tttattgtgagacgttatacactc  \n",
       "5  tttatggtgagacgttatacactc  \n",
       "6  tttgttgtgagacgttatacactc  \n",
       "7  tttgtggtgagacgttatacactc  \n",
       "8  ttttctgtgagacgttatacactc  \n",
       "9  ttttcggtgagacgttatacactc  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "doubles_df['nt_seq'] = doubles_df.mutations.apply(lambda x: get_nt_seq(wtseq, x))\n",
    "doubles_df.drop(columns='mutations', inplace=True)\n",
    "doubles_df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "98265f54-f651-422b-971a-a2de0231c378",
   "metadata": {
    "tags": []
   },
   "outputs": [
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       "      <td>ttt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>tttctggtgagacgttatacactc</td>\n",
       "      <td>1</td>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>ttt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>tttattgtgagacgttatacactc</td>\n",
       "      <td>1</td>\n",
       "      <td>double</td>\n",
       "      <td>(0, 1)</td>\n",
       "      <td>0</td>\n",
       "      <td>ttt</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55119</th>\n",
       "      <td>gattgggtgagacgttatgggcgg</td>\n",
       "      <td>2</td>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>7</td>\n",
       "      <td>cgg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55120</th>\n",
       "      <td>gattgggtgagacgttatgggagt</td>\n",
       "      <td>2</td>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>7</td>\n",
       "      <td>agt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55121</th>\n",
       "      <td>gattgggtgagacgttatgggagg</td>\n",
       "      <td>2</td>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>7</td>\n",
       "      <td>agg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55122</th>\n",
       "      <td>gattgggtgagacgttatgggggt</td>\n",
       "      <td>2</td>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>7</td>\n",
       "      <td>ggt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55123</th>\n",
       "      <td>gattgggtgagacgttatgggggg</td>\n",
       "      <td>2</td>\n",
       "      <td>double</td>\n",
       "      <td>(6, 7)</td>\n",
       "      <td>7</td>\n",
       "      <td>ggg</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55124 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                         nt_seq  mutated_codon seq_type combination  aa_pos  \\\n",
       "0      ttttttgtgagacgttatacactc              1   double      (0, 1)       0   \n",
       "1      tttttggtgagacgttatacactc              1   double      (0, 1)       0   \n",
       "2      tttcttgtgagacgttatacactc              1   double      (0, 1)       0   \n",
       "3      tttctggtgagacgttatacactc              1   double      (0, 1)       0   \n",
       "4      tttattgtgagacgttatacactc              1   double      (0, 1)       0   \n",
       "...                         ...            ...      ...         ...     ...   \n",
       "55119  gattgggtgagacgttatgggcgg              2   double      (6, 7)       7   \n",
       "55120  gattgggtgagacgttatgggagt              2   double      (6, 7)       7   \n",
       "55121  gattgggtgagacgttatgggagg              2   double      (6, 7)       7   \n",
       "55122  gattgggtgagacgttatgggggt              2   double      (6, 7)       7   \n",
       "55123  gattgggtgagacgttatgggggg              2   double      (6, 7)       7   \n",
       "\n",
       "      alt_codons  \n",
       "0            ttt  \n",
       "1            ttt  \n",
       "2            ttt  \n",
       "3            ttt  \n",
       "4            ttt  \n",
       "...          ...  \n",
       "55119        cgg  \n",
       "55120        agt  \n",
       "55121        agg  \n",
       "55122        ggt  \n",
       "55123        ggg  \n",
       "\n",
       "[55124 rows x 6 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "doubles_long = pd.wide_to_long(doubles_df, stubnames=['aa_pos', 'alt_codons'], i='nt_seq', j='mutated_codon').reset_index()\n",
    "doubles_long"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9a33671a-b8fd-4446-af09-38273fe112ea",
   "metadata": {},
   "source": [
    "## Import ortholog sequences"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "b1f01024-509f-414c-aff1-6a0d6cfdc050",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "    }\n",
       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>nt_seq</th>\n",
       "      <th>seq_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ggtgctattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>gattggatgagacaatctttgttg</td>\n",
       "      <td>ortho</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                     nt_seq seq_type\n",
       "0  ggtgttattttgaatcaacaattt    ortho\n",
       "1  ggtgctattttgaatcaacaattt    ortho\n",
       "2  gattggatgagacaatctttgttg    ortho"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ortho_df = pd.read_csv(ortho_path, header=0)\n",
    "ortho_df['seq_type'] = 'ortho'\n",
    "ortho_df.head(3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "e4ad612b-5a66-4ce4-9291-c08cf8a99fdb",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>nt_seq</th>\n",
       "      <th>seq_type</th>\n",
       "      <th>mutated_codon</th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>[1, 2, 3, 4, 5, 6, 7, 8]</td>\n",
       "      <td>[0, 1, 2, 3, 4, 5, 6, 7]</td>\n",
       "      <td>[ggt, gtt, att, ttg, aat, caa, caa, ttt]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ggtgctattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>[1, 2, 3, 4, 5, 6, 7, 8]</td>\n",
       "      <td>[0, 1, 2, 3, 4, 5, 6, 7]</td>\n",
       "      <td>[ggt, gct, att, ttg, aat, caa, caa, ttt]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>gattggatgagacaatctttgttg</td>\n",
       "      <td>ortho</td>\n",
       "      <td>[1, 2, 3, 4, 5]</td>\n",
       "      <td>[2, 4, 5, 6, 7]</td>\n",
       "      <td>[atg, caa, tct, ttg, ttg]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                     nt_seq seq_type             mutated_codon  \\\n",
       "0  ggtgttattttgaatcaacaattt    ortho  [1, 2, 3, 4, 5, 6, 7, 8]   \n",
       "1  ggtgctattttgaatcaacaattt    ortho  [1, 2, 3, 4, 5, 6, 7, 8]   \n",
       "2  gattggatgagacaatctttgttg    ortho           [1, 2, 3, 4, 5]   \n",
       "\n",
       "                     aa_pos                                alt_codons  \n",
       "0  [0, 1, 2, 3, 4, 5, 6, 7]  [ggt, gtt, att, ttg, aat, caa, caa, ttt]  \n",
       "1  [0, 1, 2, 3, 4, 5, 6, 7]  [ggt, gct, att, ttg, aat, caa, caa, ttt]  \n",
       "2           [2, 4, 5, 6, 7]                 [atg, caa, tct, ttg, ttg]  "
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ortho_df['mutated_codon'], ortho_df['aa_pos'], ortho_df['alt_codons'] = zip(*ortho_df['nt_seq'].map(lambda x: get_alt_codons(x, wtseq)))\n",
    "ortho_df.head(3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "0893d25d-f5e0-40a5-a4a2-37d77fe7ed0c",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>nt_seq</th>\n",
       "      <th>seq_type</th>\n",
       "      <th>mutated_codon</th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>ggt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>gtt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>att</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>ttg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ggtgttattttgaatcaacaattt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>5</td>\n",
       "      <td>4</td>\n",
       "      <td>aat</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>384</th>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>aat</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>385</th>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "      <td>aga</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>386</th>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>tgt</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>387</th>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "      <td>att</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>388</th>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>ortho</td>\n",
       "      <td>6</td>\n",
       "      <td>7</td>\n",
       "      <td>att</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>389 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                       nt_seq seq_type mutated_codon aa_pos alt_codons\n",
       "0    ggtgttattttgaatcaacaattt    ortho             1      0        ggt\n",
       "1    ggtgttattttgaatcaacaattt    ortho             2      1        gtt\n",
       "2    ggtgttattttgaatcaacaattt    ortho             3      2        att\n",
       "3    ggtgttattttgaatcaacaattt    ortho             4      3        ttg\n",
       "4    ggtgttattttgaatcaacaattt    ortho             5      4        aat\n",
       "..                        ...      ...           ...    ...        ...\n",
       "384  gattgggttaatagatgtattatt    ortho             2      3        aat\n",
       "385  gattgggttaatagatgtattatt    ortho             3      4        aga\n",
       "386  gattgggttaatagatgtattatt    ortho             4      5        tgt\n",
       "387  gattgggttaatagatgtattatt    ortho             5      6        att\n",
       "388  gattgggttaatagatgtattatt    ortho             6      7        att\n",
       "\n",
       "[389 rows x 5 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ortho_long = ortho_df.explode(['mutated_codon', 'aa_pos', 'alt_codons']).reset_index(drop=True)\n",
    "ortho_long"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d2847982-d298-42fd-ad5f-955a029ca4a5",
   "metadata": {},
   "source": [
    "## Concatenate all dataframes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "c24f84ec-02bc-4312-b9b9-f08722f0c245",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>seq_type</th>\n",
       "      <th>nt_seq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>WT</td>\n",
       "      <td>gattgggtgagacgttatacactc</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  seq_type                    nt_seq\n",
       "0       WT  gattgggtgagacgttatacactc"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "wt_df = pd.DataFrame.from_dict({'seq_type':['WT'], 'nt_seq':[wtseq]})\n",
    "wt_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "59e3d2b1-1bf4-4341-aea2-861127e92a38",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>seq_type</th>\n",
       "      <th>nt_seq</th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "      <th>mutated_codon</th>\n",
       "      <th>combination</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>WT</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>single</td>\n",
       "      <td>ttttgggtgagacgttatacactc</td>\n",
       "      <td>0</td>\n",
       "      <td>ttt</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>single</td>\n",
       "      <td>ttgtgggtgagacgttatacactc</td>\n",
       "      <td>0</td>\n",
       "      <td>ttg</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>single</td>\n",
       "      <td>ctttgggtgagacgttatacactc</td>\n",
       "      <td>0</td>\n",
       "      <td>ctt</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>single</td>\n",
       "      <td>ctgtgggtgagacgttatacactc</td>\n",
       "      <td>0</td>\n",
       "      <td>ctg</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55760</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>3</td>\n",
       "      <td>aat</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55761</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>4</td>\n",
       "      <td>aga</td>\n",
       "      <td>3</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55762</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>5</td>\n",
       "      <td>tgt</td>\n",
       "      <td>4</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55763</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>6</td>\n",
       "      <td>att</td>\n",
       "      <td>5</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55764</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>7</td>\n",
       "      <td>att</td>\n",
       "      <td>6</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55765 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      seq_type                    nt_seq aa_pos alt_codons mutated_codon  \\\n",
       "0           WT  gattgggtgagacgttatacactc    NaN        NaN           NaN   \n",
       "1       single  ttttgggtgagacgttatacactc      0        ttt             1   \n",
       "2       single  ttgtgggtgagacgttatacactc      0        ttg             1   \n",
       "3       single  ctttgggtgagacgttatacactc      0        ctt             1   \n",
       "4       single  ctgtgggtgagacgttatacactc      0        ctg             1   \n",
       "...        ...                       ...    ...        ...           ...   \n",
       "55760    ortho  gattgggttaatagatgtattatt      3        aat             2   \n",
       "55761    ortho  gattgggttaatagatgtattatt      4        aga             3   \n",
       "55762    ortho  gattgggttaatagatgtattatt      5        tgt             4   \n",
       "55763    ortho  gattgggttaatagatgtattatt      6        att             5   \n",
       "55764    ortho  gattgggttaatagatgtattatt      7        att             6   \n",
       "\n",
       "      combination  \n",
       "0             NaN  \n",
       "1             NaN  \n",
       "2             NaN  \n",
       "3             NaN  \n",
       "4             NaN  \n",
       "...           ...  \n",
       "55760         NaN  \n",
       "55761         NaN  \n",
       "55762         NaN  \n",
       "55763         NaN  \n",
       "55764         NaN  \n",
       "\n",
       "[55765 rows x 6 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "var_df = pd.concat([wt_df, singles_df, doubles_long, ortho_long], ignore_index = True)\n",
    "var_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "81644cee-fd37-4216-b519-9f5d9f5ea010",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "var_df.to_csv(outpath_f)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b838d40d-650a-4e9e-93fa-b4786b258c5d",
   "metadata": {},
   "source": [
    "## Checking the number of unique variants"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "f557ed48-44ff-4ade-a0ab-4c54405479e5",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>seq_type</th>\n",
       "      <th>nt_seq</th>\n",
       "      <th>aa_pos</th>\n",
       "      <th>alt_codons</th>\n",
       "      <th>mutated_codon</th>\n",
       "      <th>combination</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>WT</td>\n",
       "      <td>gattgggtgagacgttatacactc</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>single</td>\n",
       "      <td>ttttgggtgagacgttatacactc</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ttt</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>single</td>\n",
       "      <td>ttgtgggtgagacgttatacactc</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ttg</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>single</td>\n",
       "      <td>ctttgggtgagacgttatacactc</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ctt</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>single</td>\n",
       "      <td>ctgtgggtgagacgttatacactc</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ctg</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55760</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>3.0</td>\n",
       "      <td>aat</td>\n",
       "      <td>2.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55761</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>4.0</td>\n",
       "      <td>aga</td>\n",
       "      <td>3.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55762</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>5.0</td>\n",
       "      <td>tgt</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55763</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>6.0</td>\n",
       "      <td>att</td>\n",
       "      <td>5.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55764</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>7.0</td>\n",
       "      <td>att</td>\n",
       "      <td>6.0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55765 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      seq_type                    nt_seq  aa_pos alt_codons  mutated_codon  \\\n",
       "0           WT  gattgggtgagacgttatacactc     NaN        NaN            NaN   \n",
       "1       single  ttttgggtgagacgttatacactc     0.0        ttt            1.0   \n",
       "2       single  ttgtgggtgagacgttatacactc     0.0        ttg            1.0   \n",
       "3       single  ctttgggtgagacgttatacactc     0.0        ctt            1.0   \n",
       "4       single  ctgtgggtgagacgttatacactc     0.0        ctg            1.0   \n",
       "...        ...                       ...     ...        ...            ...   \n",
       "55760    ortho  gattgggttaatagatgtattatt     3.0        aat            2.0   \n",
       "55761    ortho  gattgggttaatagatgtattatt     4.0        aga            3.0   \n",
       "55762    ortho  gattgggttaatagatgtattatt     5.0        tgt            4.0   \n",
       "55763    ortho  gattgggttaatagatgtattatt     6.0        att            5.0   \n",
       "55764    ortho  gattgggttaatagatgtattatt     7.0        att            6.0   \n",
       "\n",
       "      combination  \n",
       "0             NaN  \n",
       "1             NaN  \n",
       "2             NaN  \n",
       "3             NaN  \n",
       "4             NaN  \n",
       "...           ...  \n",
       "55760         NaN  \n",
       "55761         NaN  \n",
       "55762         NaN  \n",
       "55763         NaN  \n",
       "55764         NaN  \n",
       "\n",
       "[55765 rows x 6 columns]"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "var_df = pd.read_csv(outpath_f, index_col=0)\n",
    "var_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "453fae84-cdaa-4a20-b12e-d2b8138de24b",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "def get_aa_seq(seq, cdic):\n",
    "    clist = [seq[i:i+3] for i in range(0, len(seq), 3)] # Converting nucleotide sequence to list of codons\n",
    "    return ''.join([cdic[x] for x in clist])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "1918e27d-6ecf-463b-bf1b-e7e8fd634b2c",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'DWVRRYTL'"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_aa_seq('gattgggtgagacgttatacactc', codon_dic)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "faf40c54-7923-41e1-83bb-e7961c49c0fe",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>2.0</td>\n",
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       "      <td>ortho</td>\n",
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       "      <td>DWVNRCII</td>\n",
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       "      <th>55762</th>\n",
       "      <td>ortho</td>\n",
       "      <td>gattgggttaatagatgtattatt</td>\n",
       "      <td>5.0</td>\n",
       "      <td>tgt</td>\n",
       "      <td>4.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>DWVNRCII</td>\n",
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       "      <th>55763</th>\n",
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       "      <td>5.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>DWVNRCII</td>\n",
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       "    <tr>\n",
       "      <th>55764</th>\n",
       "      <td>ortho</td>\n",
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       "      <td>att</td>\n",
       "      <td>6.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>DWVNRCII</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>55765 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      seq_type                    nt_seq  aa_pos alt_codons  mutated_codon  \\\n",
       "0           WT  gattgggtgagacgttatacactc     NaN        NaN            NaN   \n",
       "1       single  ttttgggtgagacgttatacactc     0.0        ttt            1.0   \n",
       "2       single  ttgtgggtgagacgttatacactc     0.0        ttg            1.0   \n",
       "3       single  ctttgggtgagacgttatacactc     0.0        ctt            1.0   \n",
       "4       single  ctgtgggtgagacgttatacactc     0.0        ctg            1.0   \n",
       "...        ...                       ...     ...        ...            ...   \n",
       "55760    ortho  gattgggttaatagatgtattatt     3.0        aat            2.0   \n",
       "55761    ortho  gattgggttaatagatgtattatt     4.0        aga            3.0   \n",
       "55762    ortho  gattgggttaatagatgtattatt     5.0        tgt            4.0   \n",
       "55763    ortho  gattgggttaatagatgtattatt     6.0        att            5.0   \n",
       "55764    ortho  gattgggttaatagatgtattatt     7.0        att            6.0   \n",
       "\n",
       "      combination    aa_seq  \n",
       "0             NaN  DWVRRYTL  \n",
       "1             NaN  FWVRRYTL  \n",
       "2             NaN  LWVRRYTL  \n",
       "3             NaN  LWVRRYTL  \n",
       "4             NaN  LWVRRYTL  \n",
       "...           ...       ...  \n",
       "55760         NaN  DWVNRCII  \n",
       "55761         NaN  DWVNRCII  \n",
       "55762         NaN  DWVNRCII  \n",
       "55763         NaN  DWVNRCII  \n",
       "55764         NaN  DWVNRCII  \n",
       "\n",
       "[55765 rows x 7 columns]"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "var_df['aa_seq'] = var_df.nt_seq.apply(lambda x: get_aa_seq(x, codon_dic))\n",
    "var_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "id": "b74222a8-f7c5-47b7-94ae-112554203ba0",
   "metadata": {},
   "outputs": [
    {
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>single</td>\n",
       "      <td>161</td>\n",
       "      <td>251</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  seq_type  aa_seq  nt_seq\n",
       "0       WT       1       1\n",
       "1   double   11361   27562\n",
       "2    ortho      63      63\n",
       "3   single     161     251"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "var_df.groupby('seq_type')[['aa_seq','nt_seq']].nunique().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1b307006-4ce6-426f-8bc9-a2869b7eadde",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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