codons.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from itertools import product\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "\n",
    "from Bio.Data import CodonTable"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Adapted from varalign/notebook/03_xx_Residue_Mutability.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>from_aa</th>\n",
       "      <th>to_aa</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>from_codon</th>\n",
       "      <th>to_codon</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">TTT</th>\n",
       "      <th>TTT</th>\n",
       "      <td>F</td>\n",
       "      <td>F</td>\n",
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       "    <tr>\n",
       "      <th>TTC</th>\n",
       "      <td>F</td>\n",
       "      <td>F</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTA</th>\n",
       "      <td>F</td>\n",
       "      <td>L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTG</th>\n",
       "      <td>F</td>\n",
       "      <td>L</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCT</th>\n",
       "      <td>F</td>\n",
       "      <td>S</td>\n",
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       "  </tbody>\n",
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      ],
      "text/plain": [
       "                    from_aa to_aa\n",
       "from_codon to_codon              \n",
       "TTT        TTT            F     F\n",
       "           TTC            F     F\n",
       "           TTA            F     L\n",
       "           TTG            F     L\n",
       "           TCT            F     S"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Features of the genetic code, this might be best in its own small notebook\n",
    "# want to look at the structure of the code in terms of the components of dN/dS\n",
    "# and also with respect to amino acid physical properties...\n",
    "# look at CG content\n",
    "\n",
    "# table with all codon SNPs, bi-directional\n",
    "\n",
    "genetic_code = pd.Series(CodonTable.standard_dna_table.forward_table)\n",
    "codon_mutations = pd.DataFrame(list(product(genetic_code, genetic_code)),\n",
    "                               columns=['from_aa', 'to_aa'])\n",
    "codon_mutations.index = pd.MultiIndex.from_product([genetic_code.index, genetic_code.index],\n",
    "                                                   names=['from_codon', 'to_codon'])\n",
    "codon_mutations.head()"
   ]
  },
  {
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   "execution_count": 3,
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   "outputs": [
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       "      <th>from_codon</th>\n",
       "      <th>to_codon</th>\n",
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      "text/plain": [
       "                    from_aa to_aa  n_subs\n",
       "from_codon to_codon                      \n",
       "TTT        TTT            F     F       0\n",
       "           TTC            F     F       1\n",
       "           TTA            F     L       1\n",
       "           TTG            F     L       1\n",
       "           TCT            F     S       1"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# identify snps, mnps, etc.\n",
    "def count_substitutions(s1, s2):\n",
    "    assert len(s1) == len(s2)\n",
    "    return len(s1) - sum([a == b for a,b in zip(s1, s2)])\n",
    "    \n",
    "\n",
    "n_subs = codon_mutations.index.to_frame().apply(lambda x: count_substitutions(*x),\n",
    "                                                axis=1)\n",
    "codon_mutations = codon_mutations.assign(n_subs=n_subs)\n",
    "codon_mutations.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "                    from_aa to_aa  n_subs\n",
       "from_codon to_codon                      \n",
       "TTT        TTC            F     F       1\n",
       "           TTA            F     L       1\n",
       "           TTG            F     L       1\n",
       "           TCT            F     S       1\n",
       "           TAT            F     Y       1"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# now I can identify SNPs only\n",
    "codon_mutations.query('n_subs == 1').head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
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       "      <th>from_codon</th>\n",
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      "text/plain": [
       "                    from_aa to_aa  n_subs\n",
       "from_codon to_codon                      \n",
       "TTT        TTT            F     F       0\n",
       "TTC        TTT            F     F       1\n",
       "           TTC            F     F       0\n",
       "           TTG            F     L       1\n",
       "TTA        TTT            L     F       1"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# deduplicate direction\n",
    "# pairs = list(product(codon_mutations.index.tolist(), codon_mutations.index.tolist()))\n",
    "\n",
    "def is_sorted(x):\n",
    "    return list(x) == sorted(x)  # sorted returns a list\n",
    "\n",
    "\n",
    "codon_mutations_dedupe = codon_mutations.loc[[is_sorted(x) for x in codon_mutations.index.tolist()]]\n",
    "codon_mutations_dedupe.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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       "      <th></th>\n",
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       "      <th>from_aa</th>\n",
       "      <th>to_aa</th>\n",
       "      <th>n_subs</th>\n",
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       "    <tr>\n",
       "      <th>from_codon</th>\n",
       "      <th>to_codon</th>\n",
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       "      <th rowspan=\"5\" valign=\"top\">GGG</th>\n",
       "      <th>GCG</th>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GAG</th>\n",
       "      <td>G</td>\n",
       "      <td>E</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GGT</th>\n",
       "      <td>G</td>\n",
       "      <td>G</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GGC</th>\n",
       "      <td>G</td>\n",
       "      <td>G</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>GGA</th>\n",
       "      <td>G</td>\n",
       "      <td>G</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>526 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    from_aa to_aa  n_subs\n",
       "from_codon to_codon                      \n",
       "TTT        TTC            F     F       1\n",
       "           TTA            F     L       1\n",
       "           TTG            F     L       1\n",
       "           TCT            F     S       1\n",
       "           TAT            F     Y       1\n",
       "...                     ...   ...     ...\n",
       "GGG        GCG            G     A       1\n",
       "           GAG            G     E       1\n",
       "           GGT            G     G       1\n",
       "           GGC            G     G       1\n",
       "           GGA            G     G       1\n",
       "\n",
       "[526 rows x 3 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Ok I think this is all possible SNPs\n",
    "# snps = codon_mutations_dedupe.query('n_subs == 1')\n",
    "# actually, don't think I want it deduped...\n",
    "snps = codon_mutations.query('n_subs == 1')\n",
    "snps.to_csv('snp_table.csv')\n",
    "snps"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are fewer than 9 mutations for some codons because I am ignoring stops\n",
    "and starts."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "9    43\n",
       "8    13\n",
       "7     5\n",
       "dtype: int64"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "snps.groupby('from_codon').size().value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>C</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D</th>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>E</th>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>F</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>G</th>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>H</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>I</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>K</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>18</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>M</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Q</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>R</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>18</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>14</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>T</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>V</th>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>W</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Y</th>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "to_aa     A  C  D  E  F   G  H  I  K   L  M  N   P  Q   R   S   T   V  W  Y\n",
       "from_aa                                                                    \n",
       "A        12  0  2  2  0   4  0  0  0   0  0  0   4  0   0   4   4   4  0  0\n",
       "C         0  2  0  0  2   2  0  0  0   0  0  0   0  0   2   4   0   0  2  2\n",
       "D         2  0  2  4  0   2  2  0  0   0  0  2   0  0   0   0   0   2  0  2\n",
       "E         2  0  4  2  0   2  0  0  2   0  0  0   0  2   0   0   0   2  0  0\n",
       "F         0  2  0  0  2   0  0  2  0   6  0  0   0  0   0   2   0   2  0  2\n",
       "G         4  2  2  2  0  12  0  0  0   0  0  0   0  0   6   2   0   4  1  0\n",
       "H         0  0  2  0  0   0  2  0  0   2  0  2   2  4   2   0   0   0  0  2\n",
       "I         0  0  0  0  2   0  0  6  1   4  3  2   0  0   1   2   3   3  0  0\n",
       "K         0  0  0  2  0   0  0  1  2   0  1  4   0  2   2   0   2   0  0  0\n",
       "L         0  0  0  0  6   0  2  4  0  18  2  0   4  2   4   2   0   6  1  0\n",
       "M         0  0  0  0  0   0  0  3  1   2  0  0   0  0   1   0   1   1  0  0\n",
       "N         0  0  2  0  0   0  2  2  4   0  0  2   0  0   0   2   2   0  0  2\n",
       "P         4  0  0  0  0   0  2  0  0   4  0  0  12  2   4   4   4   0  0  0\n",
       "Q         0  0  0  2  0   0  4  0  2   2  0  0   2  2   2   0   0   0  0  0\n",
       "R         0  2  0  0  0   6  2  1  2   4  1  0   4  2  18   6   2   0  2  0\n",
       "S         4  4  0  0  2   2  0  2  0   2  0  2   4  0   6  14   6   0  1  2\n",
       "T         4  0  0  0  0   0  0  3  2   0  1  2   4  0   2   6  12   0  0  0\n",
       "V         4  0  2  2  2   4  0  3  0   6  1  0   0  0   0   0   0  12  0  0\n",
       "W         0  2  0  0  0   1  0  0  0   1  0  0   0  0   2   1   0   0  0  0\n",
       "Y         0  2  2  0  2   0  2  0  0   0  0  2   0  0   0   2   0   0  0  2"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n_snps_to_mutation = pd.crosstab(snps['from_aa'], snps['to_aa'])\n",
    "n_snps_to_mutation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "from_aa\n",
       "W     7\n",
       "M     9\n",
       "Y    12\n",
       "C    14\n",
       "E    14\n",
       "K    14\n",
       "Q    14\n",
       "D    16\n",
       "F    16\n",
       "H    16\n",
       "N    16\n",
       "I    21\n",
       "G    23\n",
       "V    24\n",
       "T    24\n",
       "A    24\n",
       "P    24\n",
       "L    33\n",
       "R    34\n",
       "S    37\n",
       "dtype: int64"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "m = pd.crosstab(snps['from_aa'], snps['to_aa'])\n",
    "# m.where(np.tril(m, -1) > 0).fillna(0)\n",
    "# n possible missense, all codons\n",
    "n_mis_all_codons = (m.sum(axis=1) - np.diag(m)).sort_values()\n",
    "n_mis_all_codons"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "from_aa\n",
       "W     0\n",
       "M     0\n",
       "Y     2\n",
       "C     2\n",
       "D     2\n",
       "E     2\n",
       "F     2\n",
       "H     2\n",
       "K     2\n",
       "N     2\n",
       "Q     2\n",
       "I     6\n",
       "V    12\n",
       "T    12\n",
       "A    12\n",
       "P    12\n",
       "G    12\n",
       "S    14\n",
       "R    18\n",
       "L    18\n",
       "dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# n possible syn, all codons\n",
    "n_syn_all_codons = pd.Series(np.diag(m), m.index).sort_values()\n",
    "n_syn_all_codons"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "R    6\n",
       "S    6\n",
       "L    6\n",
       "T    4\n",
       "G    4\n",
       "A    4\n",
       "V    4\n",
       "P    4\n",
       "I    3\n",
       "D    2\n",
       "Q    2\n",
       "F    2\n",
       "C    2\n",
       "Y    2\n",
       "K    2\n",
       "H    2\n",
       "N    2\n",
       "E    2\n",
       "W    1\n",
       "M    1\n",
       "dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# n codons\n",
    "n_codons = genetic_code.value_counts()\n",
    "n_codons"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "W    0.0\n",
       "M    0.0\n",
       "Y    1.0\n",
       "C    1.0\n",
       "D    1.0\n",
       "E    1.0\n",
       "F    1.0\n",
       "H    1.0\n",
       "K    1.0\n",
       "N    1.0\n",
       "Q    1.0\n",
       "I    2.0\n",
       "S    2.3\n",
       "V    3.0\n",
       "T    3.0\n",
       "A    3.0\n",
       "P    3.0\n",
       "G    3.0\n",
       "R    3.0\n",
       "L    3.0\n",
       "dtype: float64"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n_syn_all_codons.div(n_codons).round(1).sort_values()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "L    5.5\n",
       "R    5.7\n",
       "G    5.8\n",
       "V    6.0\n",
       "T    6.0\n",
       "P    6.0\n",
       "A    6.0\n",
       "Y    6.0\n",
       "S    6.2\n",
       "I    7.0\n",
       "K    7.0\n",
       "W    7.0\n",
       "Q    7.0\n",
       "E    7.0\n",
       "C    7.0\n",
       "N    8.0\n",
       "F    8.0\n",
       "D    8.0\n",
       "H    8.0\n",
       "M    9.0\n",
       "dtype: float64"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n_mis_all_codons.div(n_codons).round(1).sort_values()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# so something with ++L may have more synonymous...\n",
    "# likewise ++H"
   ]
  }
 ],
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   "display_name": "Python [conda env:varalign-nCoV]",
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  "language_info": {
   "codemirror_mode": {
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