tests/test_escape_scores.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test computation of escape scores\n",
    "Test computation of \"escape scores\" by `CodonVariantTable.escape_scores`.\n",
    "\n",
    "First create miniature test variant table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "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>library</th>\n",
       "      <th>sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>count</th>\n",
       "      <th>variant_call_support</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>AG</td>\n",
       "      <td>20</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>AA</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib1</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>40</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>lib1</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>20</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>TA</td>\n",
       "      <td>40</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>M1I</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>TT</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>lib2</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>15</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>lib2</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>M1I</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  library sample barcode  count  variant_call_support codon_substitutions  \\\n",
       "0    lib1    pre      AG     20                     1             ATG1CAA   \n",
       "1    lib1    pre      AA     10                     1                       \n",
       "2    lib1   post      AG     30                     1             ATG1CAA   \n",
       "3    lib1   post      AA      1                     1                       \n",
       "4    lib1  post2      AG     40                     1             ATG1CAA   \n",
       "5    lib1  post2      AA     20                     1                       \n",
       "6    lib2    pre      TA     40                     1     ATG1ATC GGC2GGG   \n",
       "7    lib2    pre      TT     30                     1             ATG1ATC   \n",
       "8    lib2   post      TT     15                     1             ATG1ATC   \n",
       "9    lib2   post      TA      5                     1     ATG1ATC GGC2GGG   \n",
       "\n",
       "  aa_substitutions  n_codon_substitutions  n_aa_substitutions  \n",
       "0              M1Q                      1                   1  \n",
       "1                                       0                   0  \n",
       "2              M1Q                      1                   1  \n",
       "3                                       0                   0  \n",
       "4              M1Q                      1                   1  \n",
       "5                                       0                   0  \n",
       "6              M1I                      2                   1  \n",
       "7              M1I                      1                   1  \n",
       "8              M1I                      1                   1  \n",
       "9              M1I                      2                   1  "
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import tempfile\n",
    "\n",
    "import pandas as pd\n",
    "\n",
    "import dms_variants.codonvarianttable\n",
    "\n",
    "geneseq = \"ATGGGC\"\n",
    "\n",
    "variant_counts = pd.DataFrame.from_records(\n",
    "    [\n",
    "        (\"lib1\", \"AA\", \"\", \"pre\", 10),\n",
    "        (\"lib1\", \"AG\", \"ATG1CAA\", \"pre\", 20),\n",
    "        (\"lib2\", \"TT\", \"ATG1ATC\", \"pre\", 30),\n",
    "        (\"lib2\", \"TA\", \"ATG1ATC GGC2GGG\", \"pre\", 40),\n",
    "        (\"lib1\", \"AA\", \"\", \"post\", 1),\n",
    "        (\"lib1\", \"AG\", \"ATG1CAA\", \"post\", 30),\n",
    "        (\"lib2\", \"TT\", \"ATG1ATC\", \"post\", 15),\n",
    "        (\"lib2\", \"TA\", \"ATG1ATC GGC2GGG\", \"post\", 5),\n",
    "        (\"lib1\", \"AA\", \"\", \"post2\", 20),\n",
    "        (\"lib1\", \"AG\", \"ATG1CAA\", \"post2\", 40),\n",
    "    ],\n",
    "    columns=[\"library\", \"barcode\", \"codon_substitutions\", \"sample\", \"count\"],\n",
    ").assign(variant_call_support=1)\n",
    "\n",
    "with tempfile.NamedTemporaryFile(\"w\") as f:\n",
    "    variant_counts.to_csv(f, index=False)\n",
    "    f.flush()\n",
    "    variants = dms_variants.codonvarianttable.CodonVariantTable.from_variant_count_df(\n",
    "        variant_count_df_file=f.name, geneseq=geneseq\n",
    "    )\n",
    "\n",
    "variants.variant_count_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now compute escape scores using score type of `minus_log_bind`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>2.740562</td>\n",
       "      <td>0.318338</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.122887</td>\n",
       "      <td>0.010479</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>0.483315</td>\n",
       "      <td>0.032764</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>6.643856</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.323371</td>\n",
       "      <td>0.001021</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.319115</td>\n",
       "      <td>0.007043</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG  2.740562   0.318338   \n",
       "1  name1    lib1        pre        post      AA  0.122887   0.010479   \n",
       "2  name1    lib2        pre        post      TA  0.483315   0.032764   \n",
       "3  name1    lib2        pre        post      TT  6.643856   0.000000   \n",
       "4  name2    lib1        pre       post2      AG  0.323371   0.001021   \n",
       "5  name2    lib1        pre       post2      AA  0.319115   0.007043   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pd.DataFrame.from_records(\n",
    "    [\n",
    "        (\"name1\", \"lib1\", \"pre\", \"post\", 0.59),\n",
    "        (\"name1\", \"lib2\", \"pre\", \"post\", 0.62),\n",
    "        (\"name2\", \"lib1\", \"pre\", \"post2\", 0.2),\n",
    "    ],\n",
    "    columns=[\"name\", \"library\", \"pre_sample\", \"post_sample\", \"frac_escape\"],\n",
    ")\n",
    "\n",
    "variants.escape_scores(sample_df, score_type=\"minus_log_bind\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With a different floor:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>2.740562</td>\n",
       "      <td>0.318338</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.122887</td>\n",
       "      <td>0.010479</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>0.483315</td>\n",
       "      <td>0.032764</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>9.965784</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.323371</td>\n",
       "      <td>0.001021</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.319115</td>\n",
       "      <td>0.007043</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG  2.740562   0.318338   \n",
       "1  name1    lib1        pre        post      AA  0.122887   0.010479   \n",
       "2  name1    lib2        pre        post      TA  0.483315   0.032764   \n",
       "3  name1    lib2        pre        post      TT  9.965784   0.000000   \n",
       "4  name2    lib1        pre       post2      AG  0.323371   0.001021   \n",
       "5  name2    lib1        pre       post2      AA  0.319115   0.007043   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"minus_log_bind\", floor_B=0.001)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With a different pseudocount:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>2.587813</td>\n",
       "      <td>0.262882</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.223114</td>\n",
       "      <td>0.017847</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>0.553450</td>\n",
       "      <td>0.033410</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>6.643856</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.327060</td>\n",
       "      <td>0.001064</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.312566</td>\n",
       "      <td>0.005906</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG  2.587813   0.262882   \n",
       "1  name1    lib1        pre        post      AA  0.223114   0.017847   \n",
       "2  name1    lib2        pre        post      TA  0.553450   0.033410   \n",
       "3  name1    lib2        pre        post      TT  6.643856   0.000000   \n",
       "4  name2    lib1        pre       post2      AG  0.327060   0.001064   \n",
       "5  name2    lib1        pre       post2      AA  0.312566   0.005906   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"minus_log_bind\", pseudocount=2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "By amino-acid substitution:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>2.740562</td>\n",
       "      <td>0.318338</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td></td>\n",
       "      <td>0.122887</td>\n",
       "      <td>0.010479</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1.395929</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>70</td>\n",
       "      <td>20</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>0.323371</td>\n",
       "      <td>0.001021</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td></td>\n",
       "      <td>0.319115</td>\n",
       "      <td>0.007043</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample aa_substitutions     score  score_var  \\\n",
       "0  name1    lib1        pre        post              M1Q  2.740562   0.318338   \n",
       "1  name1    lib1        pre        post                   0.122887   0.010479   \n",
       "2  name1    lib2        pre        post              M1I  1.395929   0.000000   \n",
       "3  name2    lib1        pre       post2              M1Q  0.323371   0.001021   \n",
       "4  name2    lib1        pre       post2                   0.319115   0.007043   \n",
       "\n",
       "   pre_count  post_count  n_aa_substitutions  \n",
       "0         20          30                   1  \n",
       "1         10           1                   0  \n",
       "2         70          20                   1  \n",
       "3         20          40                   1  \n",
       "4         10          20                   0  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(\n",
    "    sample_df,\n",
    "    score_type=\"minus_log_bind\",\n",
    "    floor_B=0.001,\n",
    "    by=\"aa_substitutions\",\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now with score type `log_escape`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>-0.233831</td>\n",
       "      <td>0.010900</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>-3.614372</td>\n",
       "      <td>0.796134</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>-1.812649</td>\n",
       "      <td>0.175442</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>-2.316171</td>\n",
       "      <td>0.016332</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>-2.333235</td>\n",
       "      <td>0.118633</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG -0.233831   0.010900   \n",
       "1  name1    lib1        pre        post      AA -3.614372   0.796134   \n",
       "2  name1    lib2        pre        post      TA -1.812649   0.175442   \n",
       "3  name1    lib2        pre        post      TT  0.000000   0.000000   \n",
       "4  name2    lib1        pre       post2      AG -2.316171   0.016332   \n",
       "5  name2    lib1        pre       post2      AA -2.333235   0.118633   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"log_escape\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With a different floor:"
   ]
  },
  {
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>-0.233831</td>\n",
       "      <td>0.010900</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>-3.321928</td>\n",
       "      <td>0.240153</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>-1.812649</td>\n",
       "      <td>0.175442</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>-2.316171</td>\n",
       "      <td>0.016332</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>-2.333235</td>\n",
       "      <td>0.118633</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG -0.233831   0.010900   \n",
       "1  name1    lib1        pre        post      AA -3.321928   0.240153   \n",
       "2  name1    lib2        pre        post      TA -1.812649   0.175442   \n",
       "3  name1    lib2        pre        post      TT  0.000000   0.000000   \n",
       "4  name2    lib1        pre       post2      AG -2.316171   0.016332   \n",
       "5  name2    lib1        pre       post2      AA -2.333235   0.118633   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"log_escape\", floor_E=0.1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "With no ceiling:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>-0.233831</td>\n",
       "      <td>0.010900</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>-3.614372</td>\n",
       "      <td>0.796134</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>-1.812649</td>\n",
       "      <td>0.175442</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>0.091229</td>\n",
       "      <td>0.029460</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>-2.316171</td>\n",
       "      <td>0.016332</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>-2.333235</td>\n",
       "      <td>0.118633</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG -0.233831   0.010900   \n",
       "1  name1    lib1        pre        post      AA -3.614372   0.796134   \n",
       "2  name1    lib2        pre        post      TA -1.812649   0.175442   \n",
       "3  name1    lib2        pre        post      TT  0.091229   0.029460   \n",
       "4  name2    lib1        pre       post2      AG -2.316171   0.016332   \n",
       "5  name2    lib1        pre       post2      AA -2.333235   0.118633   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"log_escape\", ceil_E=None)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now with score type `frac_escape`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.850373</td>\n",
       "      <td>0.003728</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.081652</td>\n",
       "      <td>0.004028</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>0.284668</td>\n",
       "      <td>0.007665</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.200800</td>\n",
       "      <td>0.000314</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.198439</td>\n",
       "      <td>0.002187</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG  0.850373   0.003728   \n",
       "1  name1    lib1        pre        post      AA  0.081652   0.004028   \n",
       "2  name1    lib2        pre        post      TA  0.284668   0.007665   \n",
       "3  name1    lib2        pre        post      TT  1.000000   0.000000   \n",
       "4  name2    lib1        pre       post2      AG  0.200800   0.000314   \n",
       "5  name2    lib1        pre       post2      AA  0.198439   0.002187   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"frac_escape\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Changing ceiling and floor:"
   ]
  },
  {
   "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>name</th>\n",
       "      <th>library</th>\n",
       "      <th>pre_sample</th>\n",
       "      <th>post_sample</th>\n",
       "      <th>barcode</th>\n",
       "      <th>score</th>\n",
       "      <th>score_var</th>\n",
       "      <th>pre_count</th>\n",
       "      <th>post_count</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.850373</td>\n",
       "      <td>0.003728</td>\n",
       "      <td>20</td>\n",
       "      <td>30</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>0.001532</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TA</td>\n",
       "      <td>0.284668</td>\n",
       "      <td>0.007665</td>\n",
       "      <td>40</td>\n",
       "      <td>5</td>\n",
       "      <td>ATG1ATC GGC2GGG</td>\n",
       "      <td>2</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>name1</td>\n",
       "      <td>lib2</td>\n",
       "      <td>pre</td>\n",
       "      <td>post</td>\n",
       "      <td>TT</td>\n",
       "      <td>1.065277</td>\n",
       "      <td>0.015926</td>\n",
       "      <td>30</td>\n",
       "      <td>15</td>\n",
       "      <td>ATG1ATC</td>\n",
       "      <td>1</td>\n",
       "      <td>M1I</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AG</td>\n",
       "      <td>0.200800</td>\n",
       "      <td>0.000314</td>\n",
       "      <td>20</td>\n",
       "      <td>40</td>\n",
       "      <td>ATG1CAA</td>\n",
       "      <td>1</td>\n",
       "      <td>M1Q</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>name2</td>\n",
       "      <td>lib1</td>\n",
       "      <td>pre</td>\n",
       "      <td>post2</td>\n",
       "      <td>AA</td>\n",
       "      <td>0.198439</td>\n",
       "      <td>0.002187</td>\n",
       "      <td>10</td>\n",
       "      <td>20</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    name library pre_sample post_sample barcode     score  score_var  \\\n",
       "0  name1    lib1        pre        post      AG  0.850373   0.003728   \n",
       "1  name1    lib1        pre        post      AA  0.100000   0.001532   \n",
       "2  name1    lib2        pre        post      TA  0.284668   0.007665   \n",
       "3  name1    lib2        pre        post      TT  1.065277   0.015926   \n",
       "4  name2    lib1        pre       post2      AG  0.200800   0.000314   \n",
       "5  name2    lib1        pre       post2      AA  0.198439   0.002187   \n",
       "\n",
       "   pre_count  post_count codon_substitutions  n_codon_substitutions  \\\n",
       "0         20          30             ATG1CAA                      1   \n",
       "1         10           1                                          0   \n",
       "2         40           5     ATG1ATC GGC2GGG                      2   \n",
       "3         30          15             ATG1ATC                      1   \n",
       "4         20          40             ATG1CAA                      1   \n",
       "5         10          20                                          0   \n",
       "\n",
       "  aa_substitutions  n_aa_substitutions  \n",
       "0              M1Q                   1  \n",
       "1                                    0  \n",
       "2              M1I                   1  \n",
       "3              M1I                   1  \n",
       "4              M1Q                   1  \n",
       "5                                    0  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "variants.escape_scores(sample_df, score_type=\"frac_escape\", ceil_E=None, floor_E=0.1)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.7"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}