bio450-python-pt4-translation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "genetic_code = {\n",
    "    # this was adapted from \n",
    "    # https://gitlab.com/RebelCoder/dna-toolset/-/blob/90e8d9249c6dcc82a850aa854da4baabef98ee6f/structures.py\n",
    "    \"GCT\": \"A\", \"GCC\": \"A\", \"GCA\": \"A\", \"GCG\": \"A\",\n",
    "    \"TGT\": \"C\", \"TGC\": \"C\",\n",
    "    \"GAT\": \"D\", \"GAC\": \"D\",\n",
    "    \"GAA\": \"E\", \"GAG\": \"E\",\n",
    "    \"TTT\": \"F\", \"TTC\": \"F\",\n",
    "    \"GGT\": \"G\", \"GGC\": \"G\", \"GGA\": \"G\", \"GGG\": \"G\",\n",
    "    \"CAT\": \"H\", \"CAC\": \"H\",\n",
    "    \"ATA\": \"I\", \"ATT\": \"I\", \"ATC\": \"I\",\n",
    "    \"AAA\": \"K\", \"AAG\": \"K\",\n",
    "    \"TTA\": \"L\", \"TTG\": \"L\", \"CTT\": \"L\", \"CTC\": \"L\", \"CTA\": \"L\", \"CTG\": \"L\",\n",
    "    \"ATG\": \"M\",\n",
    "    \"AAT\": \"N\", \"AAC\": \"N\",\n",
    "    \"CCT\": \"P\", \"CCC\": \"P\", \"CCA\": \"P\", \"CCG\": \"P\",\n",
    "    \"CAA\": \"Q\", \"CAG\": \"Q\",\n",
    "    \"CGT\": \"R\", \"CGC\": \"R\", \"CGA\": \"R\", \"CGG\": \"R\", \"AGA\": \"R\", \"AGG\": \"R\",\n",
    "    \"TCT\": \"S\", \"TCC\": \"S\", \"TCA\": \"S\", \"TCG\": \"S\", \"AGT\": \"S\", \"AGC\": \"S\",\n",
    "    \"ACT\": \"T\", \"ACC\": \"T\", \"ACA\": \"T\", \"ACG\": \"T\",\n",
    "    \"GTT\": \"V\", \"GTC\": \"V\", \"GTA\": \"V\", \"GTG\": \"V\",\n",
    "    \"TGG\": \"W\",\n",
    "    \"TAT\": \"Y\", \"TAC\": \"Y\",\n",
    "    \"TAA\": \"*\", \"TAG\": \"*\", \"TGA\": \"*\"\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'TTTTATGATGT'.index('ATG')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[4, 7, 10, 13, 16, 19, 22]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(range(4, 25, 3))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "T\n"
     ]
    }
   ],
   "source": [
    "test_sequence = 'TTTTATGACCT'\n",
    "print(test_sequence[10:10+3])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'R'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "genetic_code['AGA']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "'AAA' not in 'ACGAAAT'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "def translate(sequence, genetic_code):\n",
    "    protein = []\n",
    "    \n",
    "    if 'ATG' not in sequence:\n",
    "        return protein\n",
    "    \n",
    "    first_codon_position = sequence.index('ATG')\n",
    "    \n",
    "    sequence_length = len(sequence)\n",
    "    \n",
    "    for codon_start in range(first_codon_position, sequence_length, 3):\n",
    "        codon = sequence[codon_start:codon_start+3]\n",
    "        if len(codon) == 3:\n",
    "            try:\n",
    "                amino_acid = genetic_code[codon]\n",
    "            except KeyError:\n",
    "                raise KeyError(codon + \" is not present in the genetic code.\")\n",
    "            if amino_acid == '*':\n",
    "                return protein\n",
    "            protein.append(amino_acid)\n",
    "    \n",
    "    return protein"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "ename": "KeyError",
     "evalue": "'ACU is not present in the genetic code.'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-22-02b19746c2c2>\u001b[0m in \u001b[0;36mtranslate\u001b[0;34m(sequence, genetic_code)\u001b[0m\n\u001b[1;32m     14\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 15\u001b[0;31m                 \u001b[0mamino_acid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgenetic_code\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mcodon\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     16\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyError\u001b[0m: 'ACU'",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-23-a63d615a2bdf>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mtranslate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"AGGTACGTGGAACGTACGTGACCGATGGACCACACUCATTGAGTGTGTACACACACGTGTGTGTGACACAACAAC\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgenetic_code\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m<ipython-input-22-02b19746c2c2>\u001b[0m in \u001b[0;36mtranslate\u001b[0;34m(sequence, genetic_code)\u001b[0m\n\u001b[1;32m     15\u001b[0m                 \u001b[0mamino_acid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgenetic_code\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mcodon\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     16\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 17\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcodon\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\" is not present in the genetic code.\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     18\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mamino_acid\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'*'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     19\u001b[0m                 \u001b[0;32mreturn\u001b[0m \u001b[0mprotein\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyError\u001b[0m: 'ACU is not present in the genetic code.'"
     ]
    }
   ],
   "source": [
    "translate(\"AGGTACGTGGAACGTACGTGACCGATGGACCACACUCATTGAGTGTGTACACACACGTGTGTGTGACACAACAAC\", genetic_code)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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