02_translate_peptides_and_stack.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Part 2 - Translate the peptide sequences and compute changes in the residues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from Bio.Seq import Seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>Sequence</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AACGGTGGGCGTCTTTGCTACTGTCGTCGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>138</td>\n",
       "      <td>178.0</td>\n",
       "      <td>138.0</td>\n",
       "      <td>165.0</td>\n",
       "      <td>181.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>320.0</td>\n",
       "      <td>300.0</td>\n",
       "      <td>381.0</td>\n",
       "      <td>202.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>71.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AACGGTGGGCGTCTTTGTTGCTGTCATCGCATGTTCTGCTTTTGTG...</td>\n",
       "      <td>222</td>\n",
       "      <td>261.0</td>\n",
       "      <td>231.0</td>\n",
       "      <td>314.0</td>\n",
       "      <td>331.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>485.0</td>\n",
       "      <td>573.0</td>\n",
       "      <td>570.0</td>\n",
       "      <td>1259.0</td>\n",
       "      <td>649.0</td>\n",
       "      <td>468.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACGGTGGGCGTTTTTGCTACTGCCGTCGCAGGTTCTGTGTTTGTG...</td>\n",
       "      <td>31</td>\n",
       "      <td>35.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>62.0</td>\n",
       "      <td>72.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>8.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACGGTGGGGGTCTTTGTTATTGCCTTCGCCAGTTCTACGTTTGCG...</td>\n",
       "      <td>67</td>\n",
       "      <td>68.0</td>\n",
       "      <td>63.0</td>\n",
       "      <td>68.0</td>\n",
       "      <td>73.0</td>\n",
       "      <td>72.0</td>\n",
       "      <td>121.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>143.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>149.0</td>\n",
       "      <td>114.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AATGGTGGGCGTCTTTGTTACTGTCGTCCCCGGTTCTGTGTTTGTG...</td>\n",
       "      <td>31</td>\n",
       "      <td>40.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>45.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>89.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>137.0</td>\n",
       "      <td>86.0</td>\n",
       "      <td>44.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14864</th>\n",
       "      <td>TGTGGTGGGCGTCTTTGTTACTGCCGTCGTAGGTTCTGCGTATGCG...</td>\n",
       "      <td>337</td>\n",
       "      <td>399.0</td>\n",
       "      <td>380.0</td>\n",
       "      <td>422.0</td>\n",
       "      <td>447.0</td>\n",
       "      <td>437.0</td>\n",
       "      <td>778.0</td>\n",
       "      <td>783.0</td>\n",
       "      <td>868.0</td>\n",
       "      <td>533.0</td>\n",
       "      <td>260.0</td>\n",
       "      <td>202.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14865</th>\n",
       "      <td>TGTGGTGTGCGTCGTAGTTACTGTCGTAGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>46</td>\n",
       "      <td>84.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>98.0</td>\n",
       "      <td>86.0</td>\n",
       "      <td>77.0</td>\n",
       "      <td>135.0</td>\n",
       "      <td>148.0</td>\n",
       "      <td>155.0</td>\n",
       "      <td>275.0</td>\n",
       "      <td>150.0</td>\n",
       "      <td>111.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14866</th>\n",
       "      <td>TTCGGTGGCCGTCTTAGCTATTGTCGTCGCAGGTTCTGTCTTTGCG...</td>\n",
       "      <td>1092</td>\n",
       "      <td>1475.0</td>\n",
       "      <td>1299.0</td>\n",
       "      <td>1520.0</td>\n",
       "      <td>1665.0</td>\n",
       "      <td>1474.0</td>\n",
       "      <td>2807.0</td>\n",
       "      <td>3071.0</td>\n",
       "      <td>3268.0</td>\n",
       "      <td>3284.0</td>\n",
       "      <td>1604.0</td>\n",
       "      <td>1179.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14867</th>\n",
       "      <td>TTCGGTGGGCGTCTTTGCTATTATCATAGCAGGTTCACCGTTTGTG...</td>\n",
       "      <td>16</td>\n",
       "      <td>25.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>107.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>54.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14868</th>\n",
       "      <td>TTCGGTGGGCGTCTTTGTTACTGCCGGCGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>95</td>\n",
       "      <td>134.0</td>\n",
       "      <td>85.0</td>\n",
       "      <td>117.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>104.0</td>\n",
       "      <td>183.0</td>\n",
       "      <td>210.0</td>\n",
       "      <td>248.0</td>\n",
       "      <td>68.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>22.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>14869 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                Sequence  S01_0uM_IPTG_1  \\\n",
       "0      AACGGTGGGCGTCTTTGCTACTGTCGTCGCAGGTTCTGCGTTTGCG...             138   \n",
       "1      AACGGTGGGCGTCTTTGTTGCTGTCATCGCATGTTCTGCTTTTGTG...             222   \n",
       "2      AACGGTGGGCGTTTTTGCTACTGCCGTCGCAGGTTCTGTGTTTGTG...              31   \n",
       "3      AACGGTGGGGGTCTTTGTTATTGCCTTCGCCAGTTCTACGTTTGCG...              67   \n",
       "4      AATGGTGGGCGTCTTTGTTACTGTCGTCCCCGGTTCTGTGTTTGTG...              31   \n",
       "...                                                  ...             ...   \n",
       "14864  TGTGGTGGGCGTCTTTGTTACTGCCGTCGTAGGTTCTGCGTATGCG...             337   \n",
       "14865  TGTGGTGTGCGTCGTAGTTACTGTCGTAGCAGGTTCTGCGTTTGCG...              46   \n",
       "14866  TTCGGTGGCCGTCTTAGCTATTGTCGTCGCAGGTTCTGTCTTTGCG...            1092   \n",
       "14867  TTCGGTGGGCGTCTTTGCTATTATCATAGCAGGTTCACCGTTTGTG...              16   \n",
       "14868  TTCGGTGGGCGTCTTTGTTACTGCCGGCGCAGGTTCTGCGTTTGCG...              95   \n",
       "\n",
       "       S02_0uM_IPTG_2  S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  \\\n",
       "0               178.0           138.0           165.0           181.0   \n",
       "1               261.0           231.0           314.0           331.0   \n",
       "2                35.0            23.0            31.0            28.0   \n",
       "3                68.0            63.0            68.0            73.0   \n",
       "4                40.0            29.0            48.0            45.0   \n",
       "...               ...             ...             ...             ...   \n",
       "14864           399.0           380.0           422.0           447.0   \n",
       "14865            84.0            67.0            98.0            86.0   \n",
       "14866          1475.0          1299.0          1520.0          1665.0   \n",
       "14867            25.0            47.0            33.0            42.0   \n",
       "14868           134.0            85.0           117.0           132.0   \n",
       "\n",
       "       S06_1uM_IPTG_3  S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  \\\n",
       "0               151.0            320.0            300.0            381.0   \n",
       "1               240.0            485.0            573.0            570.0   \n",
       "2                34.0             53.0             62.0             72.0   \n",
       "3                72.0            121.0            145.0            143.0   \n",
       "4                34.0             89.0             78.0             95.0   \n",
       "...               ...              ...              ...              ...   \n",
       "14864           437.0            778.0            783.0            868.0   \n",
       "14865            77.0            135.0            148.0            155.0   \n",
       "14866          1474.0           2807.0           3071.0           3268.0   \n",
       "14867            40.0             78.0             51.0             69.0   \n",
       "14868           104.0            183.0            210.0            248.0   \n",
       "\n",
       "       S10_100uM_IPTG_1  S11_100uM_IPTG_2  S12_100uM_IPTG_3  \n",
       "0                 202.0              96.0              71.0  \n",
       "1                1259.0             649.0             468.0  \n",
       "2                  31.0              12.0               8.0  \n",
       "3                 263.0             149.0             114.0  \n",
       "4                 137.0              86.0              44.0  \n",
       "...                 ...               ...               ...  \n",
       "14864             533.0             260.0             202.0  \n",
       "14865             275.0             150.0             111.0  \n",
       "14866            3284.0            1604.0            1179.0  \n",
       "14867             107.0              79.0              54.0  \n",
       "14868              68.0              39.0              22.0  \n",
       "\n",
       "[14869 rows x 13 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Load  count matrix \n",
    "counts = pd.read_table(\"/stor/work/Wilke/luiz/DMS_ML_AMP/data/counts/count_matrix.txt\", sep=\"\\s+\", engine=\"python\", header=None)\n",
    "\n",
    "# rename columns\n",
    "counts.rename(columns={0:\"Sequence\", 1:'S01_0uM_IPTG_1', 2:'S02_0uM_IPTG_2', 3:'S03_0uM_IPTG_3',\n",
    "       4:'S04_1uM_IPTG_1', 5:'S05_1uM_IPTG_2', 6:'S06_1uM_IPTG_3', 7:'S07_10uM_IPTG_1',\n",
    "       8:'S08_10uM_IPTG_2', 9:'S09_10uM_IPTG_3', 10:'S10_100uM_IPTG_1',\n",
    "       11:'S11_100uM_IPTG_2', 12:'S12_100uM_IPTG_3'}, inplace=True)\n",
    "\n",
    "counts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Translate nucleotide sequence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/stor/home/lcv454/miniconda3/envs/genomics/lib/python3.10/site-packages/Bio/Seq.py:2979: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.\n",
      "  warnings.warn(\n"
     ]
    },
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Sequence</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "      <th>peptide</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AACGGTGGGCGTCTTTGCTACTGTCGTCGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>138</td>\n",
       "      <td>178.0</td>\n",
       "      <td>138.0</td>\n",
       "      <td>165.0</td>\n",
       "      <td>181.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>320.0</td>\n",
       "      <td>300.0</td>\n",
       "      <td>381.0</td>\n",
       "      <td>202.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>NGGRLCYCRRRFCVCGGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AACGGTGGGCGTCTTTGTTGCTGTCATCGCATGTTCTGCTTTTGTG...</td>\n",
       "      <td>222</td>\n",
       "      <td>261.0</td>\n",
       "      <td>231.0</td>\n",
       "      <td>314.0</td>\n",
       "      <td>331.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>485.0</td>\n",
       "      <td>573.0</td>\n",
       "      <td>570.0</td>\n",
       "      <td>1259.0</td>\n",
       "      <td>649.0</td>\n",
       "      <td>468.0</td>\n",
       "      <td>NGGRLCCCHRMFCFCVGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACGGTGGGCGTTTTTGCTACTGCCGTCGCAGGTTCTGTGTTTGTG...</td>\n",
       "      <td>31</td>\n",
       "      <td>35.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>62.0</td>\n",
       "      <td>72.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>NGGRFCYCRRRFCVCVGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACGGTGGGGGTCTTTGTTATTGCCTTCGCCAGTTCTACGTTTGCG...</td>\n",
       "      <td>67</td>\n",
       "      <td>68.0</td>\n",
       "      <td>63.0</td>\n",
       "      <td>68.0</td>\n",
       "      <td>73.0</td>\n",
       "      <td>72.0</td>\n",
       "      <td>121.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>143.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>149.0</td>\n",
       "      <td>114.0</td>\n",
       "      <td>NGGGLCYCLRQFYVCVGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AATGGTGGGCGTCTTTGTTACTGTCGTCCCCGGTTCTGTGTTTGTG...</td>\n",
       "      <td>31</td>\n",
       "      <td>40.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>45.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>89.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>137.0</td>\n",
       "      <td>86.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>NGGRLCYCRPRFCVCVGP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14864</th>\n",
       "      <td>TGTGGTGGGCGTCTTTGTTACTGCCGTCGTAGGTTCTGCGTATGCG...</td>\n",
       "      <td>337</td>\n",
       "      <td>399.0</td>\n",
       "      <td>380.0</td>\n",
       "      <td>422.0</td>\n",
       "      <td>447.0</td>\n",
       "      <td>437.0</td>\n",
       "      <td>778.0</td>\n",
       "      <td>783.0</td>\n",
       "      <td>868.0</td>\n",
       "      <td>533.0</td>\n",
       "      <td>260.0</td>\n",
       "      <td>202.0</td>\n",
       "      <td>CGGRLCYCRRRFCVCVGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14865</th>\n",
       "      <td>TGTGGTGTGCGTCGTAGTTACTGTCGTAGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>46</td>\n",
       "      <td>84.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>98.0</td>\n",
       "      <td>86.0</td>\n",
       "      <td>77.0</td>\n",
       "      <td>135.0</td>\n",
       "      <td>148.0</td>\n",
       "      <td>155.0</td>\n",
       "      <td>275.0</td>\n",
       "      <td>150.0</td>\n",
       "      <td>111.0</td>\n",
       "      <td>CGVRRSYCRSRFCVCVGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14866</th>\n",
       "      <td>TTCGGTGGCCGTCTTAGCTATTGTCGTCGCAGGTTCTGTCTTTGCG...</td>\n",
       "      <td>1092</td>\n",
       "      <td>1475.0</td>\n",
       "      <td>1299.0</td>\n",
       "      <td>1520.0</td>\n",
       "      <td>1665.0</td>\n",
       "      <td>1474.0</td>\n",
       "      <td>2807.0</td>\n",
       "      <td>3071.0</td>\n",
       "      <td>3268.0</td>\n",
       "      <td>3284.0</td>\n",
       "      <td>1604.0</td>\n",
       "      <td>1179.0</td>\n",
       "      <td>FGGRLSYCRRRFCLCGGR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14867</th>\n",
       "      <td>TTCGGTGGGCGTCTTTGCTATTATCATAGCAGGTTCACCGTTTGTG...</td>\n",
       "      <td>16</td>\n",
       "      <td>25.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>78.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>107.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>54.0</td>\n",
       "      <td>FGGRLCYYHSRFTVCVGH</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14868</th>\n",
       "      <td>TTCGGTGGGCGTCTTTGTTACTGCCGGCGCAGGTTCTGCGTTTGCG...</td>\n",
       "      <td>95</td>\n",
       "      <td>134.0</td>\n",
       "      <td>85.0</td>\n",
       "      <td>117.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>104.0</td>\n",
       "      <td>183.0</td>\n",
       "      <td>210.0</td>\n",
       "      <td>248.0</td>\n",
       "      <td>68.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>FGGRLCYCRRRFCVCVGR</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>14869 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                Sequence  S01_0uM_IPTG_1  \\\n",
       "0      AACGGTGGGCGTCTTTGCTACTGTCGTCGCAGGTTCTGCGTTTGCG...             138   \n",
       "1      AACGGTGGGCGTCTTTGTTGCTGTCATCGCATGTTCTGCTTTTGTG...             222   \n",
       "2      AACGGTGGGCGTTTTTGCTACTGCCGTCGCAGGTTCTGTGTTTGTG...              31   \n",
       "3      AACGGTGGGGGTCTTTGTTATTGCCTTCGCCAGTTCTACGTTTGCG...              67   \n",
       "4      AATGGTGGGCGTCTTTGTTACTGTCGTCCCCGGTTCTGTGTTTGTG...              31   \n",
       "...                                                  ...             ...   \n",
       "14864  TGTGGTGGGCGTCTTTGTTACTGCCGTCGTAGGTTCTGCGTATGCG...             337   \n",
       "14865  TGTGGTGTGCGTCGTAGTTACTGTCGTAGCAGGTTCTGCGTTTGCG...              46   \n",
       "14866  TTCGGTGGCCGTCTTAGCTATTGTCGTCGCAGGTTCTGTCTTTGCG...            1092   \n",
       "14867  TTCGGTGGGCGTCTTTGCTATTATCATAGCAGGTTCACCGTTTGTG...              16   \n",
       "14868  TTCGGTGGGCGTCTTTGTTACTGCCGGCGCAGGTTCTGCGTTTGCG...              95   \n",
       "\n",
       "       S02_0uM_IPTG_2  S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  \\\n",
       "0               178.0           138.0           165.0           181.0   \n",
       "1               261.0           231.0           314.0           331.0   \n",
       "2                35.0            23.0            31.0            28.0   \n",
       "3                68.0            63.0            68.0            73.0   \n",
       "4                40.0            29.0            48.0            45.0   \n",
       "...               ...             ...             ...             ...   \n",
       "14864           399.0           380.0           422.0           447.0   \n",
       "14865            84.0            67.0            98.0            86.0   \n",
       "14866          1475.0          1299.0          1520.0          1665.0   \n",
       "14867            25.0            47.0            33.0            42.0   \n",
       "14868           134.0            85.0           117.0           132.0   \n",
       "\n",
       "       S06_1uM_IPTG_3  S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  \\\n",
       "0               151.0            320.0            300.0            381.0   \n",
       "1               240.0            485.0            573.0            570.0   \n",
       "2                34.0             53.0             62.0             72.0   \n",
       "3                72.0            121.0            145.0            143.0   \n",
       "4                34.0             89.0             78.0             95.0   \n",
       "...               ...              ...              ...              ...   \n",
       "14864           437.0            778.0            783.0            868.0   \n",
       "14865            77.0            135.0            148.0            155.0   \n",
       "14866          1474.0           2807.0           3071.0           3268.0   \n",
       "14867            40.0             78.0             51.0             69.0   \n",
       "14868           104.0            183.0            210.0            248.0   \n",
       "\n",
       "       S10_100uM_IPTG_1  S11_100uM_IPTG_2  S12_100uM_IPTG_3  \\\n",
       "0                 202.0              96.0              71.0   \n",
       "1                1259.0             649.0             468.0   \n",
       "2                  31.0              12.0               8.0   \n",
       "3                 263.0             149.0             114.0   \n",
       "4                 137.0              86.0              44.0   \n",
       "...                 ...               ...               ...   \n",
       "14864             533.0             260.0             202.0   \n",
       "14865             275.0             150.0             111.0   \n",
       "14866            3284.0            1604.0            1179.0   \n",
       "14867             107.0              79.0              54.0   \n",
       "14868              68.0              39.0              22.0   \n",
       "\n",
       "                  peptide  \n",
       "0      NGGRLCYCRRRFCVCGGR  \n",
       "1      NGGRLCCCHRMFCFCVGR  \n",
       "2      NGGRFCYCRRRFCVCVGR  \n",
       "3      NGGGLCYCLRQFYVCVGR  \n",
       "4      NGGRLCYCRPRFCVCVGP  \n",
       "...                   ...  \n",
       "14864  CGGRLCYCRRRFCVCVGR  \n",
       "14865  CGVRRSYCRSRFCVCVGR  \n",
       "14866  FGGRLSYCRRRFCLCGGR  \n",
       "14867  FGGRLCYYHSRFTVCVGH  \n",
       "14868  FGGRLCYCRRRFCVCVGR  \n",
       "\n",
       "[14869 rows x 14 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Translate nucleotide sequence\n",
    "counts['peptide'] = [\"\".join(Seq(sq).translate(to_stop=True)) for sq in counts[\"Sequence\"]]\n",
    "counts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Stacking read counts\n",
    "This stacked dataframe will be used to compute diferencial expression analysis for each peptide."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>peptide</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td></td>\n",
       "      <td>2042</td>\n",
       "      <td>2673.0</td>\n",
       "      <td>2430.0</td>\n",
       "      <td>2873.0</td>\n",
       "      <td>3093.0</td>\n",
       "      <td>2614.0</td>\n",
       "      <td>4801.0</td>\n",
       "      <td>5656.0</td>\n",
       "      <td>5990.0</td>\n",
       "      <td>12997.0</td>\n",
       "      <td>6094.0</td>\n",
       "      <td>5096.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>173</td>\n",
       "      <td>196.0</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>412.0</td>\n",
       "      <td>459.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>71.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AVGVFAIAVADSVFAQDVKSTCRH</td>\n",
       "      <td>300</td>\n",
       "      <td>418.0</td>\n",
       "      <td>309.0</td>\n",
       "      <td>379.0</td>\n",
       "      <td>384.0</td>\n",
       "      <td>354.0</td>\n",
       "      <td>665.0</td>\n",
       "      <td>711.0</td>\n",
       "      <td>775.0</td>\n",
       "      <td>2007.0</td>\n",
       "      <td>1072.0</td>\n",
       "      <td>711.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AVGVFVIAVAGSAFVYDVKSTCRH</td>\n",
       "      <td>208</td>\n",
       "      <td>271.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>260.0</td>\n",
       "      <td>329.0</td>\n",
       "      <td>281.0</td>\n",
       "      <td>488.0</td>\n",
       "      <td>445.0</td>\n",
       "      <td>520.0</td>\n",
       "      <td>1406.0</td>\n",
       "      <td>710.0</td>\n",
       "      <td>523.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AVPVFVIAVAGSVFA</td>\n",
       "      <td>158</td>\n",
       "      <td>212.0</td>\n",
       "      <td>192.0</td>\n",
       "      <td>261.0</td>\n",
       "      <td>274.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>368.0</td>\n",
       "      <td>445.0</td>\n",
       "      <td>461.0</td>\n",
       "      <td>1041.0</td>\n",
       "      <td>526.0</td>\n",
       "      <td>454.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7795</th>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>448</td>\n",
       "      <td>577.0</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>1174.0</td>\n",
       "      <td>1165.0</td>\n",
       "      <td>970.0</td>\n",
       "      <td>589.0</td>\n",
       "      <td>370.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7796</th>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>56</td>\n",
       "      <td>71.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>361.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>130.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7797</th>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>319</td>\n",
       "      <td>435.0</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>846.0</td>\n",
       "      <td>992.0</td>\n",
       "      <td>884.0</td>\n",
       "      <td>450.0</td>\n",
       "      <td>330.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7798</th>\n",
       "      <td>YGGRLCYCRRRFCVSV</td>\n",
       "      <td>149</td>\n",
       "      <td>208.0</td>\n",
       "      <td>172.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>183.0</td>\n",
       "      <td>189.0</td>\n",
       "      <td>316.0</td>\n",
       "      <td>383.0</td>\n",
       "      <td>350.0</td>\n",
       "      <td>525.0</td>\n",
       "      <td>270.0</td>\n",
       "      <td>223.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7799</th>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>41</td>\n",
       "      <td>55.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>90.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7800 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                       peptide  S01_0uM_IPTG_1  S02_0uM_IPTG_2  \\\n",
       "0                                         2042          2673.0   \n",
       "1           AGGRLCYCRRRFCVCVGR             173           196.0   \n",
       "2     AVGVFAIAVADSVFAQDVKSTCRH             300           418.0   \n",
       "3     AVGVFVIAVAGSAFVYDVKSTCRH             208           271.0   \n",
       "4              AVPVFVIAVAGSVFA             158           212.0   \n",
       "...                        ...             ...             ...   \n",
       "7795        YGGLLCYCRRRSCVCVGR             448           577.0   \n",
       "7796        YGGRLCYCGRRLCVCVGR              56            71.0   \n",
       "7797        YGGRLCYCHHRICVCVGR             319           435.0   \n",
       "7798          YGGRLCYCRRRFCVSV             149           208.0   \n",
       "7799        YGGRVCYCRRRFGVCVGR              41            55.0   \n",
       "\n",
       "      S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  S06_1uM_IPTG_3  \\\n",
       "0             2430.0          2873.0          3093.0          2614.0   \n",
       "1              193.0           242.0           213.0           236.0   \n",
       "2              309.0           379.0           384.0           354.0   \n",
       "3              211.0           260.0           329.0           281.0   \n",
       "4              192.0           261.0           274.0           236.0   \n",
       "...              ...             ...             ...             ...   \n",
       "7795           481.0           592.0           626.0           580.0   \n",
       "7796            81.0            67.0            83.0            76.0   \n",
       "7797           393.0           438.0           508.0           424.0   \n",
       "7798           172.0           191.0           183.0           189.0   \n",
       "7799            48.0            74.0            57.0            67.0   \n",
       "\n",
       "      S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  S10_100uM_IPTG_1  \\\n",
       "0              4801.0           5656.0           5990.0           12997.0   \n",
       "1               409.0            412.0            459.0             240.0   \n",
       "2               665.0            711.0            775.0            2007.0   \n",
       "3               488.0            445.0            520.0            1406.0   \n",
       "4               368.0            445.0            461.0            1041.0   \n",
       "...               ...              ...              ...               ...   \n",
       "7795           1082.0           1174.0           1165.0             970.0   \n",
       "7796            129.0            139.0            151.0             361.0   \n",
       "7797            885.0            846.0            992.0             884.0   \n",
       "7798            316.0            383.0            350.0             525.0   \n",
       "7799            126.0            118.0            125.0             265.0   \n",
       "\n",
       "      S11_100uM_IPTG_2  S12_100uM_IPTG_3  \n",
       "0               6094.0            5096.0  \n",
       "1                145.0              71.0  \n",
       "2               1072.0             711.0  \n",
       "3                710.0             523.0  \n",
       "4                526.0             454.0  \n",
       "...                ...               ...  \n",
       "7795             589.0             370.0  \n",
       "7796             211.0             130.0  \n",
       "7797             450.0             330.0  \n",
       "7798             270.0             223.0  \n",
       "7799             132.0              90.0  \n",
       "\n",
       "[7800 rows x 13 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Stacking (sum) all the read counts that translate the same peptide\n",
    "cols = ['S01_0uM_IPTG_1', 'S02_0uM_IPTG_2', 'S03_0uM_IPTG_3',\n",
    "       'S04_1uM_IPTG_1', 'S05_1uM_IPTG_2', 'S06_1uM_IPTG_3', 'S07_10uM_IPTG_1',\n",
    "       'S08_10uM_IPTG_2', 'S09_10uM_IPTG_3', 'S10_100uM_IPTG_1',\n",
    "       'S11_100uM_IPTG_2', 'S12_100uM_IPTG_3']\n",
    "\n",
    "df_stacked = counts.groupby([\"peptide\"], as_index=False)[cols].sum().copy()\n",
    "\n",
    "df_stacked"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>peptide</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>len_pep</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>173</td>\n",
       "      <td>18</td>\n",
       "      <td>196.0</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>412.0</td>\n",
       "      <td>459.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>71.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CCGRLCYCRRRSCVCVGR</td>\n",
       "      <td>20</td>\n",
       "      <td>18</td>\n",
       "      <td>32.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>22.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CDGRLCYCRRRFCVCVGR</td>\n",
       "      <td>33</td>\n",
       "      <td>18</td>\n",
       "      <td>69.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>110.0</td>\n",
       "      <td>113.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>CDGRLCYCRSGLSVSVGH</td>\n",
       "      <td>101</td>\n",
       "      <td>18</td>\n",
       "      <td>126.0</td>\n",
       "      <td>136.0</td>\n",
       "      <td>141.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>288.0</td>\n",
       "      <td>295.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>223.0</td>\n",
       "      <td>204.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CGARFCYSRRRFCVCVGR</td>\n",
       "      <td>163</td>\n",
       "      <td>18</td>\n",
       "      <td>207.0</td>\n",
       "      <td>194.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>373.0</td>\n",
       "      <td>388.0</td>\n",
       "      <td>400.0</td>\n",
       "      <td>559.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>218.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7794</th>\n",
       "      <td>YGGHLCSCRRRLCVTVGR</td>\n",
       "      <td>331</td>\n",
       "      <td>18</td>\n",
       "      <td>466.0</td>\n",
       "      <td>408.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>430.0</td>\n",
       "      <td>789.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>937.0</td>\n",
       "      <td>1276.0</td>\n",
       "      <td>596.0</td>\n",
       "      <td>501.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7795</th>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>448</td>\n",
       "      <td>18</td>\n",
       "      <td>577.0</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>1174.0</td>\n",
       "      <td>1165.0</td>\n",
       "      <td>970.0</td>\n",
       "      <td>589.0</td>\n",
       "      <td>370.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7796</th>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>56</td>\n",
       "      <td>18</td>\n",
       "      <td>71.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>361.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>130.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7797</th>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>319</td>\n",
       "      <td>18</td>\n",
       "      <td>435.0</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>846.0</td>\n",
       "      <td>992.0</td>\n",
       "      <td>884.0</td>\n",
       "      <td>450.0</td>\n",
       "      <td>330.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7799</th>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>41</td>\n",
       "      <td>18</td>\n",
       "      <td>55.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>90.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7104 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 peptide  S01_0uM_IPTG_1  len_pep  S02_0uM_IPTG_2  \\\n",
       "1     AGGRLCYCRRRFCVCVGR             173       18           196.0   \n",
       "6     CCGRLCYCRRRSCVCVGR              20       18            32.0   \n",
       "7     CDGRLCYCRRRFCVCVGR              33       18            69.0   \n",
       "8     CDGRLCYCRSGLSVSVGH             101       18           126.0   \n",
       "9     CGARFCYSRRRFCVCVGR             163       18           207.0   \n",
       "...                  ...             ...      ...             ...   \n",
       "7794  YGGHLCSCRRRLCVTVGR             331       18           466.0   \n",
       "7795  YGGLLCYCRRRSCVCVGR             448       18           577.0   \n",
       "7796  YGGRLCYCGRRLCVCVGR              56       18            71.0   \n",
       "7797  YGGRLCYCHHRICVCVGR             319       18           435.0   \n",
       "7799  YGGRVCYCRRRFGVCVGR              41       18            55.0   \n",
       "\n",
       "      S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  S06_1uM_IPTG_3  \\\n",
       "1              193.0           242.0           213.0           236.0   \n",
       "6               32.0            36.0            35.0            25.0   \n",
       "7               35.0            47.0            44.0            51.0   \n",
       "8              136.0           141.0           139.0           145.0   \n",
       "9              194.0           191.0           242.0           195.0   \n",
       "...              ...             ...             ...             ...   \n",
       "7794           408.0           438.0           500.0           430.0   \n",
       "7795           481.0           592.0           626.0           580.0   \n",
       "7796            81.0            67.0            83.0            76.0   \n",
       "7797           393.0           438.0           508.0           424.0   \n",
       "7799            48.0            74.0            57.0            67.0   \n",
       "\n",
       "      S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  S10_100uM_IPTG_1  \\\n",
       "1               409.0            412.0            459.0             240.0   \n",
       "6                51.0             71.0             76.0              69.0   \n",
       "7                95.0            101.0            110.0             113.0   \n",
       "8               330.0            288.0            295.0             405.0   \n",
       "9               373.0            388.0            400.0             559.0   \n",
       "...               ...              ...              ...               ...   \n",
       "7794            789.0            892.0            937.0            1276.0   \n",
       "7795           1082.0           1174.0           1165.0             970.0   \n",
       "7796            129.0            139.0            151.0             361.0   \n",
       "7797            885.0            846.0            992.0             884.0   \n",
       "7799            126.0            118.0            125.0             265.0   \n",
       "\n",
       "      S11_100uM_IPTG_2  S12_100uM_IPTG_3  \n",
       "1                145.0              71.0  \n",
       "6                 36.0              22.0  \n",
       "7                 61.0              51.0  \n",
       "8                223.0             204.0  \n",
       "9                263.0             218.0  \n",
       "...                ...               ...  \n",
       "7794             596.0             501.0  \n",
       "7795             589.0             370.0  \n",
       "7796             211.0             130.0  \n",
       "7797             450.0             330.0  \n",
       "7799             132.0              90.0  \n",
       "\n",
       "[7104 rows x 14 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# adding pep length column\n",
    "df_stacked.insert(2, 'len_pep', df_stacked.peptide.str.len())\n",
    "df_stacked = df_stacked.query('len_pep == 18').copy()\n",
    "df_stacked"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>peptide</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>len_pep</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "      <th>Mean_0IPTG_reads</th>\n",
       "      <th>Mean_1IPTG_reads</th>\n",
       "      <th>Mean_10IPTG_reads</th>\n",
       "      <th>Mean_100IPTG_reads</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>173</td>\n",
       "      <td>18</td>\n",
       "      <td>196.0</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>412.0</td>\n",
       "      <td>459.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>187.0</td>\n",
       "      <td>230.0</td>\n",
       "      <td>427.0</td>\n",
       "      <td>152.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CCGRLCYCRRRSCVCVGR</td>\n",
       "      <td>20</td>\n",
       "      <td>18</td>\n",
       "      <td>32.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>66.0</td>\n",
       "      <td>42.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CDGRLCYCRRRFCVCVGR</td>\n",
       "      <td>33</td>\n",
       "      <td>18</td>\n",
       "      <td>69.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>110.0</td>\n",
       "      <td>113.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>102.0</td>\n",
       "      <td>75.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>CDGRLCYCRSGLSVSVGH</td>\n",
       "      <td>101</td>\n",
       "      <td>18</td>\n",
       "      <td>126.0</td>\n",
       "      <td>136.0</td>\n",
       "      <td>141.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>288.0</td>\n",
       "      <td>295.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>223.0</td>\n",
       "      <td>204.0</td>\n",
       "      <td>121.0</td>\n",
       "      <td>142.0</td>\n",
       "      <td>304.0</td>\n",
       "      <td>277.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CGARFCYSRRRFCVCVGR</td>\n",
       "      <td>163</td>\n",
       "      <td>18</td>\n",
       "      <td>207.0</td>\n",
       "      <td>194.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>373.0</td>\n",
       "      <td>388.0</td>\n",
       "      <td>400.0</td>\n",
       "      <td>559.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>218.0</td>\n",
       "      <td>188.0</td>\n",
       "      <td>209.0</td>\n",
       "      <td>387.0</td>\n",
       "      <td>347.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7794</th>\n",
       "      <td>YGGHLCSCRRRLCVTVGR</td>\n",
       "      <td>331</td>\n",
       "      <td>18</td>\n",
       "      <td>466.0</td>\n",
       "      <td>408.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>430.0</td>\n",
       "      <td>789.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>937.0</td>\n",
       "      <td>1276.0</td>\n",
       "      <td>596.0</td>\n",
       "      <td>501.0</td>\n",
       "      <td>402.0</td>\n",
       "      <td>456.0</td>\n",
       "      <td>873.0</td>\n",
       "      <td>791.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7795</th>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>448</td>\n",
       "      <td>18</td>\n",
       "      <td>577.0</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>1174.0</td>\n",
       "      <td>1165.0</td>\n",
       "      <td>970.0</td>\n",
       "      <td>589.0</td>\n",
       "      <td>370.0</td>\n",
       "      <td>502.0</td>\n",
       "      <td>599.0</td>\n",
       "      <td>1140.0</td>\n",
       "      <td>643.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7796</th>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>56</td>\n",
       "      <td>18</td>\n",
       "      <td>71.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>361.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>75.0</td>\n",
       "      <td>140.0</td>\n",
       "      <td>234.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7797</th>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>319</td>\n",
       "      <td>18</td>\n",
       "      <td>435.0</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>846.0</td>\n",
       "      <td>992.0</td>\n",
       "      <td>884.0</td>\n",
       "      <td>450.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>382.0</td>\n",
       "      <td>457.0</td>\n",
       "      <td>908.0</td>\n",
       "      <td>555.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7799</th>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>41</td>\n",
       "      <td>18</td>\n",
       "      <td>55.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>90.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>66.0</td>\n",
       "      <td>123.0</td>\n",
       "      <td>162.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7104 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 peptide  S01_0uM_IPTG_1  len_pep  S02_0uM_IPTG_2  \\\n",
       "1     AGGRLCYCRRRFCVCVGR             173       18           196.0   \n",
       "6     CCGRLCYCRRRSCVCVGR              20       18            32.0   \n",
       "7     CDGRLCYCRRRFCVCVGR              33       18            69.0   \n",
       "8     CDGRLCYCRSGLSVSVGH             101       18           126.0   \n",
       "9     CGARFCYSRRRFCVCVGR             163       18           207.0   \n",
       "...                  ...             ...      ...             ...   \n",
       "7794  YGGHLCSCRRRLCVTVGR             331       18           466.0   \n",
       "7795  YGGLLCYCRRRSCVCVGR             448       18           577.0   \n",
       "7796  YGGRLCYCGRRLCVCVGR              56       18            71.0   \n",
       "7797  YGGRLCYCHHRICVCVGR             319       18           435.0   \n",
       "7799  YGGRVCYCRRRFGVCVGR              41       18            55.0   \n",
       "\n",
       "      S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  S06_1uM_IPTG_3  \\\n",
       "1              193.0           242.0           213.0           236.0   \n",
       "6               32.0            36.0            35.0            25.0   \n",
       "7               35.0            47.0            44.0            51.0   \n",
       "8              136.0           141.0           139.0           145.0   \n",
       "9              194.0           191.0           242.0           195.0   \n",
       "...              ...             ...             ...             ...   \n",
       "7794           408.0           438.0           500.0           430.0   \n",
       "7795           481.0           592.0           626.0           580.0   \n",
       "7796            81.0            67.0            83.0            76.0   \n",
       "7797           393.0           438.0           508.0           424.0   \n",
       "7799            48.0            74.0            57.0            67.0   \n",
       "\n",
       "      S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  S10_100uM_IPTG_1  \\\n",
       "1               409.0            412.0            459.0             240.0   \n",
       "6                51.0             71.0             76.0              69.0   \n",
       "7                95.0            101.0            110.0             113.0   \n",
       "8               330.0            288.0            295.0             405.0   \n",
       "9               373.0            388.0            400.0             559.0   \n",
       "...               ...              ...              ...               ...   \n",
       "7794            789.0            892.0            937.0            1276.0   \n",
       "7795           1082.0           1174.0           1165.0             970.0   \n",
       "7796            129.0            139.0            151.0             361.0   \n",
       "7797            885.0            846.0            992.0             884.0   \n",
       "7799            126.0            118.0            125.0             265.0   \n",
       "\n",
       "      S11_100uM_IPTG_2  S12_100uM_IPTG_3  Mean_0IPTG_reads  Mean_1IPTG_reads  \\\n",
       "1                145.0              71.0             187.0             230.0   \n",
       "6                 36.0              22.0              28.0              32.0   \n",
       "7                 61.0              51.0              46.0              47.0   \n",
       "8                223.0             204.0             121.0             142.0   \n",
       "9                263.0             218.0             188.0             209.0   \n",
       "...                ...               ...               ...               ...   \n",
       "7794             596.0             501.0             402.0             456.0   \n",
       "7795             589.0             370.0             502.0             599.0   \n",
       "7796             211.0             130.0              69.0              75.0   \n",
       "7797             450.0             330.0             382.0             457.0   \n",
       "7799             132.0              90.0              48.0              66.0   \n",
       "\n",
       "      Mean_10IPTG_reads  Mean_100IPTG_reads  \n",
       "1                 427.0               152.0  \n",
       "6                  66.0                42.0  \n",
       "7                 102.0                75.0  \n",
       "8                 304.0               277.0  \n",
       "9                 387.0               347.0  \n",
       "...                 ...                 ...  \n",
       "7794              873.0               791.0  \n",
       "7795             1140.0               643.0  \n",
       "7796              140.0               234.0  \n",
       "7797              908.0               555.0  \n",
       "7799              123.0               162.0  \n",
       "\n",
       "[7104 rows x 18 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# creating columns with mean df_stacked for each group\n",
    "df_stacked[\"Mean_0IPTG_reads\"] = ((df_stacked['S01_0uM_IPTG_1'] + df_stacked['S02_0uM_IPTG_2'] + df_stacked['S03_0uM_IPTG_3']) /3).round()\n",
    "df_stacked[\"Mean_1IPTG_reads\"] = ((df_stacked['S04_1uM_IPTG_1'] + df_stacked['S05_1uM_IPTG_2'] + df_stacked['S06_1uM_IPTG_3']) /3).round()\n",
    "df_stacked[\"Mean_10IPTG_reads\"] = ((df_stacked['S07_10uM_IPTG_1'] + df_stacked['S08_10uM_IPTG_2'] + df_stacked['S09_10uM_IPTG_3']) /3).round()\n",
    "df_stacked[\"Mean_100IPTG_reads\"] = ((df_stacked['S10_100uM_IPTG_1'] + df_stacked['S11_100uM_IPTG_2'] + df_stacked['S12_100uM_IPTG_3']) /3).round()\n",
    "\n",
    "df_stacked"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Creating functions to compare peptides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'-RR-I---PL--Y-----'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# def to find the differences between the residues\n",
    "idx = \"RRRRICYCPLRFYVCVGR\"\n",
    "\n",
    "def diff_func(idxx):\n",
    "    pg1 = \"RGGRLCYCRRRFCVCVGR\"\n",
    "    idx = idxx\n",
    "    diff = []\n",
    "    for i in range(0, len(pg1)):\n",
    "        aa = idx[i]\n",
    "        pg_aa = pg1[i]\n",
    "        \n",
    "        if pg_aa == aa:\n",
    "            diff.append(\"-\")\n",
    "        else:\n",
    "            diff.append(aa)\n",
    "    diff_seq = \"\".join(diff)\n",
    "    return diff_seq\n",
    "\n",
    "\n",
    "diff_func(idx)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# function to add the number of changes in each peptide\n",
    "def changesFunc(idxx):\n",
    "    pg1 = \"RGGRLCYCRRRFCVCVGR\"\n",
    "    idx = idxx\n",
    "    changes = 0\n",
    "    for i in range(0, len(pg1)):\n",
    "        aa = idx[i]\n",
    "        pg_aa = pg1[i]\n",
    "        \n",
    "        if pg_aa != aa:\n",
    "            changes+=1\n",
    "    return changes\n",
    "\n",
    "changesFunc(idx)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Applying changes into the new data frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>peptide</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>len_pep</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "      <th>Mean_0IPTG_reads</th>\n",
       "      <th>Mean_1IPTG_reads</th>\n",
       "      <th>Mean_10IPTG_reads</th>\n",
       "      <th>Mean_100IPTG_reads</th>\n",
       "      <th>diff_in_seq</th>\n",
       "      <th>changes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>173</td>\n",
       "      <td>18</td>\n",
       "      <td>196.0</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>412.0</td>\n",
       "      <td>459.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>187.0</td>\n",
       "      <td>230.0</td>\n",
       "      <td>427.0</td>\n",
       "      <td>152.0</td>\n",
       "      <td>A-----------------</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>CCGRLCYCRRRSCVCVGR</td>\n",
       "      <td>20</td>\n",
       "      <td>18</td>\n",
       "      <td>32.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>66.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>CC---------S------</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>CDGRLCYCRRRFCVCVGR</td>\n",
       "      <td>33</td>\n",
       "      <td>18</td>\n",
       "      <td>69.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>110.0</td>\n",
       "      <td>113.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>102.0</td>\n",
       "      <td>75.0</td>\n",
       "      <td>CD----------------</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>CDGRLCYCRSGLSVSVGH</td>\n",
       "      <td>101</td>\n",
       "      <td>18</td>\n",
       "      <td>126.0</td>\n",
       "      <td>136.0</td>\n",
       "      <td>141.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>288.0</td>\n",
       "      <td>295.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>223.0</td>\n",
       "      <td>204.0</td>\n",
       "      <td>121.0</td>\n",
       "      <td>142.0</td>\n",
       "      <td>304.0</td>\n",
       "      <td>277.0</td>\n",
       "      <td>CD-------SGLS-S--H</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>CGARFCYSRRRFCVCVGR</td>\n",
       "      <td>163</td>\n",
       "      <td>18</td>\n",
       "      <td>207.0</td>\n",
       "      <td>194.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>373.0</td>\n",
       "      <td>388.0</td>\n",
       "      <td>400.0</td>\n",
       "      <td>559.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>218.0</td>\n",
       "      <td>188.0</td>\n",
       "      <td>209.0</td>\n",
       "      <td>387.0</td>\n",
       "      <td>347.0</td>\n",
       "      <td>C-A-F--S----------</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7794</th>\n",
       "      <td>YGGHLCSCRRRLCVTVGR</td>\n",
       "      <td>331</td>\n",
       "      <td>18</td>\n",
       "      <td>466.0</td>\n",
       "      <td>408.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>430.0</td>\n",
       "      <td>789.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>937.0</td>\n",
       "      <td>1276.0</td>\n",
       "      <td>596.0</td>\n",
       "      <td>501.0</td>\n",
       "      <td>402.0</td>\n",
       "      <td>456.0</td>\n",
       "      <td>873.0</td>\n",
       "      <td>791.0</td>\n",
       "      <td>Y--H--S----L--T---</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7795</th>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>448</td>\n",
       "      <td>18</td>\n",
       "      <td>577.0</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>1174.0</td>\n",
       "      <td>1165.0</td>\n",
       "      <td>970.0</td>\n",
       "      <td>589.0</td>\n",
       "      <td>370.0</td>\n",
       "      <td>502.0</td>\n",
       "      <td>599.0</td>\n",
       "      <td>1140.0</td>\n",
       "      <td>643.0</td>\n",
       "      <td>Y--L-------S------</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7796</th>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>56</td>\n",
       "      <td>18</td>\n",
       "      <td>71.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>361.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>130.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>75.0</td>\n",
       "      <td>140.0</td>\n",
       "      <td>234.0</td>\n",
       "      <td>Y-------G--L------</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7797</th>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>319</td>\n",
       "      <td>18</td>\n",
       "      <td>435.0</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>846.0</td>\n",
       "      <td>992.0</td>\n",
       "      <td>884.0</td>\n",
       "      <td>450.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>382.0</td>\n",
       "      <td>457.0</td>\n",
       "      <td>908.0</td>\n",
       "      <td>555.0</td>\n",
       "      <td>Y-------HH-I------</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7799</th>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>41</td>\n",
       "      <td>18</td>\n",
       "      <td>55.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>90.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>66.0</td>\n",
       "      <td>123.0</td>\n",
       "      <td>162.0</td>\n",
       "      <td>Y---V-------G-----</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7104 rows × 20 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 peptide  S01_0uM_IPTG_1  len_pep  S02_0uM_IPTG_2  \\\n",
       "1     AGGRLCYCRRRFCVCVGR             173       18           196.0   \n",
       "6     CCGRLCYCRRRSCVCVGR              20       18            32.0   \n",
       "7     CDGRLCYCRRRFCVCVGR              33       18            69.0   \n",
       "8     CDGRLCYCRSGLSVSVGH             101       18           126.0   \n",
       "9     CGARFCYSRRRFCVCVGR             163       18           207.0   \n",
       "...                  ...             ...      ...             ...   \n",
       "7794  YGGHLCSCRRRLCVTVGR             331       18           466.0   \n",
       "7795  YGGLLCYCRRRSCVCVGR             448       18           577.0   \n",
       "7796  YGGRLCYCGRRLCVCVGR              56       18            71.0   \n",
       "7797  YGGRLCYCHHRICVCVGR             319       18           435.0   \n",
       "7799  YGGRVCYCRRRFGVCVGR              41       18            55.0   \n",
       "\n",
       "      S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  S06_1uM_IPTG_3  \\\n",
       "1              193.0           242.0           213.0           236.0   \n",
       "6               32.0            36.0            35.0            25.0   \n",
       "7               35.0            47.0            44.0            51.0   \n",
       "8              136.0           141.0           139.0           145.0   \n",
       "9              194.0           191.0           242.0           195.0   \n",
       "...              ...             ...             ...             ...   \n",
       "7794           408.0           438.0           500.0           430.0   \n",
       "7795           481.0           592.0           626.0           580.0   \n",
       "7796            81.0            67.0            83.0            76.0   \n",
       "7797           393.0           438.0           508.0           424.0   \n",
       "7799            48.0            74.0            57.0            67.0   \n",
       "\n",
       "      S07_10uM_IPTG_1  S08_10uM_IPTG_2  S09_10uM_IPTG_3  S10_100uM_IPTG_1  \\\n",
       "1               409.0            412.0            459.0             240.0   \n",
       "6                51.0             71.0             76.0              69.0   \n",
       "7                95.0            101.0            110.0             113.0   \n",
       "8               330.0            288.0            295.0             405.0   \n",
       "9               373.0            388.0            400.0             559.0   \n",
       "...               ...              ...              ...               ...   \n",
       "7794            789.0            892.0            937.0            1276.0   \n",
       "7795           1082.0           1174.0           1165.0             970.0   \n",
       "7796            129.0            139.0            151.0             361.0   \n",
       "7797            885.0            846.0            992.0             884.0   \n",
       "7799            126.0            118.0            125.0             265.0   \n",
       "\n",
       "      S11_100uM_IPTG_2  S12_100uM_IPTG_3  Mean_0IPTG_reads  Mean_1IPTG_reads  \\\n",
       "1                145.0              71.0             187.0             230.0   \n",
       "6                 36.0              22.0              28.0              32.0   \n",
       "7                 61.0              51.0              46.0              47.0   \n",
       "8                223.0             204.0             121.0             142.0   \n",
       "9                263.0             218.0             188.0             209.0   \n",
       "...                ...               ...               ...               ...   \n",
       "7794             596.0             501.0             402.0             456.0   \n",
       "7795             589.0             370.0             502.0             599.0   \n",
       "7796             211.0             130.0              69.0              75.0   \n",
       "7797             450.0             330.0             382.0             457.0   \n",
       "7799             132.0              90.0              48.0              66.0   \n",
       "\n",
       "      Mean_10IPTG_reads  Mean_100IPTG_reads         diff_in_seq  changes  \n",
       "1                 427.0               152.0  A-----------------        1  \n",
       "6                  66.0                42.0  CC---------S------        3  \n",
       "7                 102.0                75.0  CD----------------        2  \n",
       "8                 304.0               277.0  CD-------SGLS-S--H        8  \n",
       "9                 387.0               347.0  C-A-F--S----------        4  \n",
       "...                 ...                 ...                 ...      ...  \n",
       "7794              873.0               791.0  Y--H--S----L--T---        5  \n",
       "7795             1140.0               643.0  Y--L-------S------        3  \n",
       "7796              140.0               234.0  Y-------G--L------        3  \n",
       "7797              908.0               555.0  Y-------HH-I------        4  \n",
       "7799              123.0               162.0  Y---V-------G-----        3  \n",
       "\n",
       "[7104 rows x 20 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# applying functions\n",
    "df_stacked[\"diff_in_seq\"] = [diff_func(x) for x in df_stacked[\"peptide\"]]\n",
    "df_stacked[\"changes\"] = [changesFunc(x) for x in df_stacked[\"peptide\"]]\n",
    "df_stacked"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\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>ID</th>\n",
       "      <th>peptide</th>\n",
       "      <th>S01_0uM_IPTG_1</th>\n",
       "      <th>len_pep</th>\n",
       "      <th>S02_0uM_IPTG_2</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>...</th>\n",
       "      <th>P10</th>\n",
       "      <th>P11</th>\n",
       "      <th>P12</th>\n",
       "      <th>P13</th>\n",
       "      <th>P14</th>\n",
       "      <th>P15</th>\n",
       "      <th>P16</th>\n",
       "      <th>P17</th>\n",
       "      <th>P18</th>\n",
       "      <th>P19</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>173</td>\n",
       "      <td>18</td>\n",
       "      <td>196.0</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>6</td>\n",
       "      <td>CCGRLCYCRRRSCVCVGR</td>\n",
       "      <td>20</td>\n",
       "      <td>18</td>\n",
       "      <td>32.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>S</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>7</td>\n",
       "      <td>CDGRLCYCRRRFCVCVGR</td>\n",
       "      <td>33</td>\n",
       "      <td>18</td>\n",
       "      <td>69.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>8</td>\n",
       "      <td>CDGRLCYCRSGLSVSVGH</td>\n",
       "      <td>101</td>\n",
       "      <td>18</td>\n",
       "      <td>126.0</td>\n",
       "      <td>136.0</td>\n",
       "      <td>141.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>...</td>\n",
       "      <td>S</td>\n",
       "      <td>G</td>\n",
       "      <td>L</td>\n",
       "      <td>S</td>\n",
       "      <td>-</td>\n",
       "      <td>S</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>H</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>9</td>\n",
       "      <td>CGARFCYSRRRFCVCVGR</td>\n",
       "      <td>163</td>\n",
       "      <td>18</td>\n",
       "      <td>207.0</td>\n",
       "      <td>194.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>373.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7099</th>\n",
       "      <td>7794</td>\n",
       "      <td>YGGHLCSCRRRLCVTVGR</td>\n",
       "      <td>331</td>\n",
       "      <td>18</td>\n",
       "      <td>466.0</td>\n",
       "      <td>408.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>430.0</td>\n",
       "      <td>789.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>L</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>T</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7100</th>\n",
       "      <td>7795</td>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>448</td>\n",
       "      <td>18</td>\n",
       "      <td>577.0</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>S</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7101</th>\n",
       "      <td>7796</td>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>56</td>\n",
       "      <td>18</td>\n",
       "      <td>71.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>L</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7102</th>\n",
       "      <td>7797</td>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>319</td>\n",
       "      <td>18</td>\n",
       "      <td>435.0</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>...</td>\n",
       "      <td>H</td>\n",
       "      <td>-</td>\n",
       "      <td>I</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7103</th>\n",
       "      <td>7799</td>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>41</td>\n",
       "      <td>18</td>\n",
       "      <td>55.0</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>...</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>G</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7104 rows × 41 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        ID             peptide  S01_0uM_IPTG_1  len_pep  S02_0uM_IPTG_2  \\\n",
       "0        1  AGGRLCYCRRRFCVCVGR             173       18           196.0   \n",
       "1        6  CCGRLCYCRRRSCVCVGR              20       18            32.0   \n",
       "2        7  CDGRLCYCRRRFCVCVGR              33       18            69.0   \n",
       "3        8  CDGRLCYCRSGLSVSVGH             101       18           126.0   \n",
       "4        9  CGARFCYSRRRFCVCVGR             163       18           207.0   \n",
       "...    ...                 ...             ...      ...             ...   \n",
       "7099  7794  YGGHLCSCRRRLCVTVGR             331       18           466.0   \n",
       "7100  7795  YGGLLCYCRRRSCVCVGR             448       18           577.0   \n",
       "7101  7796  YGGRLCYCGRRLCVCVGR              56       18            71.0   \n",
       "7102  7797  YGGRLCYCHHRICVCVGR             319       18           435.0   \n",
       "7103  7799  YGGRVCYCRRRFGVCVGR              41       18            55.0   \n",
       "\n",
       "      S03_0uM_IPTG_3  S04_1uM_IPTG_1  S05_1uM_IPTG_2  S06_1uM_IPTG_3  \\\n",
       "0              193.0           242.0           213.0           236.0   \n",
       "1               32.0            36.0            35.0            25.0   \n",
       "2               35.0            47.0            44.0            51.0   \n",
       "3              136.0           141.0           139.0           145.0   \n",
       "4              194.0           191.0           242.0           195.0   \n",
       "...              ...             ...             ...             ...   \n",
       "7099           408.0           438.0           500.0           430.0   \n",
       "7100           481.0           592.0           626.0           580.0   \n",
       "7101            81.0            67.0            83.0            76.0   \n",
       "7102           393.0           438.0           508.0           424.0   \n",
       "7103            48.0            74.0            57.0            67.0   \n",
       "\n",
       "      S07_10uM_IPTG_1  ...  P10  P11  P12  P13  P14  P15  P16  P17  P18 P19  \n",
       "0               409.0  ...    -    -    -    -    -    -    -    -    -      \n",
       "1                51.0  ...    -    -    S    -    -    -    -    -    -      \n",
       "2                95.0  ...    -    -    -    -    -    -    -    -    -      \n",
       "3               330.0  ...    S    G    L    S    -    S    -    -    H      \n",
       "4               373.0  ...    -    -    -    -    -    -    -    -    -      \n",
       "...               ...  ...  ...  ...  ...  ...  ...  ...  ...  ...  ...  ..  \n",
       "7099            789.0  ...    -    -    L    -    -    T    -    -    -      \n",
       "7100           1082.0  ...    -    -    S    -    -    -    -    -    -      \n",
       "7101            129.0  ...    -    -    L    -    -    -    -    -    -      \n",
       "7102            885.0  ...    H    -    I    -    -    -    -    -    -      \n",
       "7103            126.0  ...    -    -    -    G    -    -    -    -    -      \n",
       "\n",
       "[7104 rows x 41 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Merging dataframes\n",
    "new_diff = df_stacked[\"diff_in_seq\"].str.split(\"\", n= -1, expand = True)\n",
    "new_df_stacked = pd.merge(df_stacked, new_diff, left_index=True, right_index=True)\n",
    "new_df_stacked.reset_index(drop=False, inplace=True)\n",
    "\n",
    "# rename columns positions\n",
    "new_cols = {'index':'ID', 0:'P0', 1:'P1', 2:'P2', 3:'P3', 4:'P4', 5:'P5', 6:'P6', 7:'P7', 8:'P8', 9:'P9', 10:'P10', 11:'P11', 12:'P12', 13:'P13', 14:'P14', 15:'P15', 16:'P16', 17:'P17', 18:'P18', 19:'P19'}\n",
    "new_df_stacked.rename(columns=new_cols, inplace=True)\n",
    "new_df_stacked"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    .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>ID</th>\n",
       "      <th>peptide</th>\n",
       "      <th>len_pep</th>\n",
       "      <th>diff_in_seq</th>\n",
       "      <th>changes</th>\n",
       "      <th>P1</th>\n",
       "      <th>P2</th>\n",
       "      <th>P3</th>\n",
       "      <th>P4</th>\n",
       "      <th>P5</th>\n",
       "      <th>...</th>\n",
       "      <th>S03_0uM_IPTG_3</th>\n",
       "      <th>S04_1uM_IPTG_1</th>\n",
       "      <th>S05_1uM_IPTG_2</th>\n",
       "      <th>S06_1uM_IPTG_3</th>\n",
       "      <th>S07_10uM_IPTG_1</th>\n",
       "      <th>S08_10uM_IPTG_2</th>\n",
       "      <th>S09_10uM_IPTG_3</th>\n",
       "      <th>S10_100uM_IPTG_1</th>\n",
       "      <th>S11_100uM_IPTG_2</th>\n",
       "      <th>S12_100uM_IPTG_3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>AGGRLCYCRRRFCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>A-----------------</td>\n",
       "      <td>1</td>\n",
       "      <td>A</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>193.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>213.0</td>\n",
       "      <td>236.0</td>\n",
       "      <td>409.0</td>\n",
       "      <td>412.0</td>\n",
       "      <td>459.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>71.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>6</td>\n",
       "      <td>CCGRLCYCRRRSCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>CC---------S------</td>\n",
       "      <td>3</td>\n",
       "      <td>C</td>\n",
       "      <td>C</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>32.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>71.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>22.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>7</td>\n",
       "      <td>CDGRLCYCRRRFCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>CD----------------</td>\n",
       "      <td>2</td>\n",
       "      <td>C</td>\n",
       "      <td>D</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>35.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>101.0</td>\n",
       "      <td>110.0</td>\n",
       "      <td>113.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>8</td>\n",
       "      <td>CDGRLCYCRSGLSVSVGH</td>\n",
       "      <td>18</td>\n",
       "      <td>CD-------SGLS-S--H</td>\n",
       "      <td>8</td>\n",
       "      <td>C</td>\n",
       "      <td>D</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>136.0</td>\n",
       "      <td>141.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>145.0</td>\n",
       "      <td>330.0</td>\n",
       "      <td>288.0</td>\n",
       "      <td>295.0</td>\n",
       "      <td>405.0</td>\n",
       "      <td>223.0</td>\n",
       "      <td>204.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>9</td>\n",
       "      <td>CGARFCYSRRRFCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>C-A-F--S----------</td>\n",
       "      <td>4</td>\n",
       "      <td>C</td>\n",
       "      <td>-</td>\n",
       "      <td>A</td>\n",
       "      <td>-</td>\n",
       "      <td>F</td>\n",
       "      <td>...</td>\n",
       "      <td>194.0</td>\n",
       "      <td>191.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>195.0</td>\n",
       "      <td>373.0</td>\n",
       "      <td>388.0</td>\n",
       "      <td>400.0</td>\n",
       "      <td>559.0</td>\n",
       "      <td>263.0</td>\n",
       "      <td>218.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7099</th>\n",
       "      <td>7794</td>\n",
       "      <td>YGGHLCSCRRRLCVTVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>Y--H--S----L--T---</td>\n",
       "      <td>5</td>\n",
       "      <td>Y</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>H</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>408.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>500.0</td>\n",
       "      <td>430.0</td>\n",
       "      <td>789.0</td>\n",
       "      <td>892.0</td>\n",
       "      <td>937.0</td>\n",
       "      <td>1276.0</td>\n",
       "      <td>596.0</td>\n",
       "      <td>501.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7100</th>\n",
       "      <td>7795</td>\n",
       "      <td>YGGLLCYCRRRSCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>Y--L-------S------</td>\n",
       "      <td>3</td>\n",
       "      <td>Y</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>L</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>481.0</td>\n",
       "      <td>592.0</td>\n",
       "      <td>626.0</td>\n",
       "      <td>580.0</td>\n",
       "      <td>1082.0</td>\n",
       "      <td>1174.0</td>\n",
       "      <td>1165.0</td>\n",
       "      <td>970.0</td>\n",
       "      <td>589.0</td>\n",
       "      <td>370.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7101</th>\n",
       "      <td>7796</td>\n",
       "      <td>YGGRLCYCGRRLCVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>Y-------G--L------</td>\n",
       "      <td>3</td>\n",
       "      <td>Y</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>81.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>83.0</td>\n",
       "      <td>76.0</td>\n",
       "      <td>129.0</td>\n",
       "      <td>139.0</td>\n",
       "      <td>151.0</td>\n",
       "      <td>361.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>130.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7102</th>\n",
       "      <td>7797</td>\n",
       "      <td>YGGRLCYCHHRICVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>Y-------HH-I------</td>\n",
       "      <td>4</td>\n",
       "      <td>Y</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>...</td>\n",
       "      <td>393.0</td>\n",
       "      <td>438.0</td>\n",
       "      <td>508.0</td>\n",
       "      <td>424.0</td>\n",
       "      <td>885.0</td>\n",
       "      <td>846.0</td>\n",
       "      <td>992.0</td>\n",
       "      <td>884.0</td>\n",
       "      <td>450.0</td>\n",
       "      <td>330.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7103</th>\n",
       "      <td>7799</td>\n",
       "      <td>YGGRVCYCRRRFGVCVGR</td>\n",
       "      <td>18</td>\n",
       "      <td>Y---V-------G-----</td>\n",
       "      <td>3</td>\n",
       "      <td>Y</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>-</td>\n",
       "      <td>V</td>\n",
       "      <td>...</td>\n",
       "      <td>48.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>57.0</td>\n",
       "      <td>67.0</td>\n",
       "      <td>126.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>132.0</td>\n",
       "      <td>90.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7104 rows × 39 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        ID             peptide  len_pep         diff_in_seq  changes P1 P2 P3  \\\n",
       "0        1  AGGRLCYCRRRFCVCVGR       18  A-----------------        1  A  -  -   \n",
       "1        6  CCGRLCYCRRRSCVCVGR       18  CC---------S------        3  C  C  -   \n",
       "2        7  CDGRLCYCRRRFCVCVGR       18  CD----------------        2  C  D  -   \n",
       "3        8  CDGRLCYCRSGLSVSVGH       18  CD-------SGLS-S--H        8  C  D  -   \n",
       "4        9  CGARFCYSRRRFCVCVGR       18  C-A-F--S----------        4  C  -  A   \n",
       "...    ...                 ...      ...                 ...      ... .. .. ..   \n",
       "7099  7794  YGGHLCSCRRRLCVTVGR       18  Y--H--S----L--T---        5  Y  -  -   \n",
       "7100  7795  YGGLLCYCRRRSCVCVGR       18  Y--L-------S------        3  Y  -  -   \n",
       "7101  7796  YGGRLCYCGRRLCVCVGR       18  Y-------G--L------        3  Y  -  -   \n",
       "7102  7797  YGGRLCYCHHRICVCVGR       18  Y-------HH-I------        4  Y  -  -   \n",
       "7103  7799  YGGRVCYCRRRFGVCVGR       18  Y---V-------G-----        3  Y  -  -   \n",
       "\n",
       "     P4 P5  ... S03_0uM_IPTG_3 S04_1uM_IPTG_1 S05_1uM_IPTG_2 S06_1uM_IPTG_3  \\\n",
       "0     -  -  ...          193.0          242.0          213.0          236.0   \n",
       "1     -  -  ...           32.0           36.0           35.0           25.0   \n",
       "2     -  -  ...           35.0           47.0           44.0           51.0   \n",
       "3     -  -  ...          136.0          141.0          139.0          145.0   \n",
       "4     -  F  ...          194.0          191.0          242.0          195.0   \n",
       "...  .. ..  ...            ...            ...            ...            ...   \n",
       "7099  H  -  ...          408.0          438.0          500.0          430.0   \n",
       "7100  L  -  ...          481.0          592.0          626.0          580.0   \n",
       "7101  -  -  ...           81.0           67.0           83.0           76.0   \n",
       "7102  -  -  ...          393.0          438.0          508.0          424.0   \n",
       "7103  -  V  ...           48.0           74.0           57.0           67.0   \n",
       "\n",
       "     S07_10uM_IPTG_1 S08_10uM_IPTG_2 S09_10uM_IPTG_3 S10_100uM_IPTG_1  \\\n",
       "0              409.0           412.0           459.0            240.0   \n",
       "1               51.0            71.0            76.0             69.0   \n",
       "2               95.0           101.0           110.0            113.0   \n",
       "3              330.0           288.0           295.0            405.0   \n",
       "4              373.0           388.0           400.0            559.0   \n",
       "...              ...             ...             ...              ...   \n",
       "7099           789.0           892.0           937.0           1276.0   \n",
       "7100          1082.0          1174.0          1165.0            970.0   \n",
       "7101           129.0           139.0           151.0            361.0   \n",
       "7102           885.0           846.0           992.0            884.0   \n",
       "7103           126.0           118.0           125.0            265.0   \n",
       "\n",
       "     S11_100uM_IPTG_2 S12_100uM_IPTG_3  \n",
       "0               145.0             71.0  \n",
       "1                36.0             22.0  \n",
       "2                61.0             51.0  \n",
       "3               223.0            204.0  \n",
       "4               263.0            218.0  \n",
       "...               ...              ...  \n",
       "7099            596.0            501.0  \n",
       "7100            589.0            370.0  \n",
       "7101            211.0            130.0  \n",
       "7102            450.0            330.0  \n",
       "7103            132.0             90.0  \n",
       "\n",
       "[7104 rows x 39 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Filtring just the columns of interest\n",
    "cols = ['ID', 'peptide', 'len_pep', 'diff_in_seq', 'changes',\"P1\",\"P2\",\"P3\",\"P4\",\"P5\",\"P6\",\"P7\",\"P8\",\"P9\",\"P10\",\"P11\",\"P12\",\"P13\",\"P14\",\"P15\",\"P16\",\"P17\",\"P18\",\n",
    "        'Mean_0IPTG_reads','Mean_1IPTG_reads', 'Mean_10IPTG_reads', 'Mean_100IPTG_reads', \n",
    "        'S01_0uM_IPTG_1', 'S02_0uM_IPTG_2', 'S03_0uM_IPTG_3',\n",
    "        'S04_1uM_IPTG_1', 'S05_1uM_IPTG_2', 'S06_1uM_IPTG_3',\n",
    "        'S07_10uM_IPTG_1', 'S08_10uM_IPTG_2','S09_10uM_IPTG_3',\n",
    "        'S10_100uM_IPTG_1', 'S11_100uM_IPTG_2','S12_100uM_IPTG_3'\n",
    "        ]\n",
    "\n",
    "new_df_stacked = new_df_stacked[cols]\n",
    "new_df_stacked"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Saving results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "#new_df_stacked.to_csv(\"results/counts_matrix_stacked.csv\", header=True, index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The End"
   ]
  }
 ],
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