rosalind_008_prot.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Importing the \"json\" library to read codon table\n",
    "\n",
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Function definition\n",
    "\n",
    "def rna_to_protein(rna_string):\n",
    "\n",
    "    with open('Data/rna_codon_table.txt') as f:\n",
    "        rna_codon_table = json.loads(f.read())\n",
    "\n",
    "    protein = \"\"\n",
    "\n",
    "    for i in range(0, len(rna_string) - 2, 3):\n",
    "\n",
    "        codon = rna_string[i:i+3]\n",
    "        amino_acid = rna_codon_table[codon]\n",
    "\n",
    "        # Stopping condition\n",
    "        if amino_acid == \"Stop\":\n",
    "            break\n",
    "\n",
    "        protein += rna_codon_table[codon]\n",
    "\n",
    "    return(protein)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Reading the input file\n",
    "\n",
    "with open('Data/008_rosalind_prot.txt') as data:\n",
    "    rna_string = data.read().splitlines()[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'MVIRSLATPLHRDSRISEPRGRLFTMVAASIFSWNCIRAPSFYTCSVGTAGEPIRGAGTHFCWSPNALAMVCGQVRLNHHRSTRKPTRPTCALRGLTAGTLLQRGVFVRYNLEERLHGLRLKLCGRTSLTLYDLDIGIGHDFRYTRVLKANSGRSYSSLHPDAVPLGGCGIRQKSPPCVKRSRVKEPPAIHLRISREEFVLRYVELLSKDPSDVNLMARPNVGLAAIPSGVVCVNWLSYRKLNPLSVIQLGHTGWQHCSNGENLMHVPGTNGTHFSYQRLNCDNVIVAVAAIFLEIVAAHARRELARCPAGAKRAALEFHPSSCCLHQLRGLSVPSRVLPIKYDSLTTSEKRLTDEGVYNITYGIDDPTSSDRTRYSRYSIIASAILSRAKLPVLDLPLTRLSTPYPEIWESAPIPLQLWYISQLNRFYCRGLTISHQKLCSAIHPSGPWEFVLLGPACNGIATVCRRSRHTLAHWAYWVLTRATQLVYPTSKPTTCREIFNSAPGKYEENFNFPLNQPRFLPACDRSKLHNSQLNAHRQFTRRSATEMPYIRLSIRNRGDQGLRKMPTICDELINVISDELILFFHRHCLHTSVGPLRSSQPTRTGKQPGPVRRVSPTTSSPTFHLTEPSRYLNRRHNVHTIPVSPVGSRALHTFAVFPPRCLAVHGIEQHYTRCSGRNDALRPLYRAMEAHECQLGRQQHSSLSSIRRSHAICCDVYSLESTASRSPTHCLKIRSKNCEGKRRTKTAFCTAILRITAAVIASRGSQELARTGAARMRAQVQTTKPGRLYEPQRRAIIDILKSTLYDVKNQSILTYSVTNDSISQVSHPPCLWKFTDGNARNFDSVTRVSIGGKLHCENLIFAGLWSKWSEQRPGPRSKGLSVTSRPGILYAQCHSPEYRSGARLREHFKVDSKGSLYCRNNVPPRFVPFGGTGTSLSHRIFRSRSCPLEPGHPLANSLNCHLESEHPGTNYKGAFQRIFNNVSWVSSEASKCGPTGNVVFVSYPISPTAKAGSFELYTRRLRTHESPCASNIATSRESAIRAKESFKSRRCGAILSARMLVLPALQQGLQASPRVLQSTYLLLGINHKALPGDRIELGARLPIFSGPMTTASVRFGWIALVVLVHPHPNGTRRLKRPESKSRFKTKTKTAPLTERDLGRDELRIGFERLRCHQTTPHSLCIRVYLRPTGYRSRYGFPGSARELRRARGFHPFSLSPGSQGRIRLTRVRRPIPTTRCSYSFLGRVVARHPVSPELRWYSQGFSCWHWQALNGRSGIGELHHSNGWENDSTPRVGKKARASSSASGLCRTYAKCLKASVNKIILGIKRLECVKVEPFFFEFPSWMRRNTYELLCAMHSFSLASCFCRAPDVTSCNVSAPISCTDVICRTQSGDVELTSPADSSSPEALRLFFRRILRCVWDSTCHLIRERNRGVKWALVLWVTRPLRVVTLANVAYPRSIPVTPRNLYLYFSELNPGLGYPWERPPHTLVLCLVSVTAYTTLQRHPRRAFIWVCYLWVILQLCGYAVDGGAFMVALACSRQGGPKGRSRNPTARAIFTLTDSFLRLLGMPVRSHGQRIDNASEHLLYFLQDSKTSHNRLGVIRSAPYYYDHEQCVNMLLYPLGCTREKPLHRDAKAGVHTTLFAQFDPGLALDLRETHRYKTVWCKRLSNNSISVECSPGQVRSLGIHRASVTTFLTVGPPLFSGGIEYSRDGPGVSLLPDPNESPGGPEAGRERRHLFHSSNGLTFSASNSLKWLGVAYVGNELLSSGYENINHDKRNYERFPGNVGLTKNIDVLVFRITVCIHTNVKRACLRVLAIILGTNMKICRCKLLRSRLQDIRDYSVIVASNRCLVWWPGVAEGVTYAINTSSLNTNHSGVKPMWETDSKGVTSRFISHFTAGSDIATLASRIAGNKYPVPGTKAITRPIRSPCDAKHAFLGNVSDLGILSATRQAIAPLCSPLSPSTTECFPNNVLESCCCRLQRSPSCRDEHFAMGIASSCIKRWKRFRGTRLMRRRRFCCSLGTLVTSGNLTRQGTHPIWFARRKRPIRNQTVRVNQLSDRLICPVLPFCTCWNDRAGRLLHPESILRCDTTSNQAGFVLYYLCSISIILLMWLHSMTLEFGVNLSMSTAGRRHVGTGHSSTHTFRLSASAHPRVRMPHPIVLKRTRCERSTTWERGSRRQGAWRSGAEVQTSFIAYVELIVNDSVYIQPFSWFEEPRWLDPRRRCKFSSRTSSCSGSYDDSFGGSRQAPAQRRSLGHCFCLETLYKTSVVTFKDGYLTNLLLPSSLFSLIKSSLPTERITFAGSRAISYQAEHSGTFPHQPRVFFIVGRCTYHRKLESRLQRFTTYAICNKLRNVEDCSYQEGMLLAVASIHPATAFGCRGHLKMLFGFRSVCFRIQTIQNPPTPPHFICTANRVLHTSRNRMAELAVARWIKSSWFSEGPQGNDVNIGYKPSNLLDQRCIPRRPLMSVCFAHAFQDDYTTLLRNLKFGHLEPLARKSCIQVSLARHPAPGSYFDLTGHKGPGTRPGLHRYGPMNRTPPRGGRAYRVTRPVAYIQVSMGLAPIDRYPTCPRSDIHLEHQGESTRHGIMTSPTTTRSSPMILLALTILDTWESSIGIKLLRPNFPATQSSNRSSTSGPNTGSVATSGCCAGHRDCVDASTLISVGLHRLGSNTDTANCRPRMKRPRPRVAGGDRYKTRSASKTLRPEGSCACLSATCEPSLWKLRSYLKYPCRLSSRPDIIQAQQGYRERLEIPRATTCRSRFHRERLFSLHTWHVGRSAPRLRGLLANHICPDEESDPYFITEGSTRGFLDVHLLGTPRWGTHVYAARLTAEYLMRYYVKRLYAIARCYANQCGYGLALLALDLCYAIKSYASLKWVGWPLLSIKVHNVVAKPHRFETAFGRTLRLLIYDSVSNDREKREMSSARGARCDGVGTSGGTASREVPPGAHISYFLIVPLGLACHVVFRSPDHCSYWGEAHPNSFGIPSVDSSAPFLTVFIGSCILANLPGRSTELSTVELMRLAEYCCIFALTRC'"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Applying the function\n",
    "\n",
    "rna_to_protein(rna_string)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "base",
   "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": "3.9.16"
  },
  "orig_nbformat": 4
 },
 "nbformat": 4,
 "nbformat_minor": 2
}