Programming Examination- Toluwani Wilson.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "aggregate-breach",
   "metadata": {},
   "outputs": [
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "please enter a DNA sequence. 'A','T','C','G','A','T','C','G','A','T','C','A','G','A','T','T','T','A','A','A','C','G','G','C','A','T','A','T','C','A','T','A','G','C','A','C','G','T','A','C','A','T','G','A','C','G'\n"
     ]
    },
    {
     "ename": "KeyError",
     "evalue": "\"'\"",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-1-e7398e914f90>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     12\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mrevCompDNA\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     13\u001b[0m \u001b[0mDNA\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0minput\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'please enter a DNA sequence.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 14\u001b[0;31m \u001b[0mrevCompDNA\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreverse_complement\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDNA\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     15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<ipython-input-1-e7398e914f90>\u001b[0m in \u001b[0;36mreverse_complement\u001b[0;34m(DNA)\u001b[0m\n\u001b[1;32m      8\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mDNA\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mreverse_complement\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDNA\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[0;32m---> 10\u001b[0;31m     \u001b[0mcompDNA\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcomplement\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDNA\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     11\u001b[0m     \u001b[0mrevCompDNA\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreverse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcompDNA\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mrevCompDNA\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m<ipython-input-1-e7398e914f90>\u001b[0m in \u001b[0;36mcomplement\u001b[0;34m(DNA)\u001b[0m\n\u001b[1;32m      3\u001b[0m     \u001b[0mcompDNA\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      4\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mDNA\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m         \u001b[0mcompDNA\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0mcomp\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mb\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      6\u001b[0m     \u001b[0;32mreturn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcompDNA\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mreverse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mDNA\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[0;31mKeyError\u001b[0m: \"'\""
     ]
    }
   ],
   "source": [
    "def complement(DNA):\n",
    "    comp = {'A':'T', 'C':'G', 'G':'C', 'T':'A'}\n",
    "    compDNA = ''\n",
    "    for b in DNA:\n",
    "        compDNA += comp[b]\n",
    "    return(compDNA)\n",
    "def reverse(DNA):\n",
    "    return DNA[::-1]\n",
    "def reverse_complement(DNA):\n",
    "    compDNA = complement(DNA)\n",
    "    revCompDNA = reverse(compDNA)\n",
    "    return revCompDNA\n",
    "DNA = input('please enter a DNA sequence.')\n",
    "revCompDNA = reverse_complement(DNA)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "secondary-airline",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4\n",
      "5\n",
      "6\n",
      "7\n",
      "8\n",
      "9\n",
      "10\n"
     ]
    }
   ],
   "source": [
    "#for loop for values 4-10\n",
    "for values in range(4,11):\n",
    "    print(values)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "premium-crown",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "1\n",
      "2\n",
      "3\n",
      "4\n",
      "5\n"
     ]
    }
   ],
   "source": [
    "x = 0\n",
    "while x < 6:\n",
    "    print(x)\n",
    "    x += 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "measured-cooperative",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The total number of characters in this DNA string:588\n"
     ]
    }
   ],
   "source": [
    "#>MH403560.1 Human rotavirus A isolate KEN/0509/2011 VP4 (P) gene, partial cds\n",
    "DNA='CTCGATGGTCCTTATCAACCAACAAATTTTAAGCCACCAAATGATTACTGGATATTATTGAATCCAACTAATCAACAAGTTGTATTAGAGGGTACCAATAAAACTGATGTTTGGGTTGCTTTATTACTTGTTGAACCAAACGTAACCAATCAAAGTAGACAATACACATTATTTGGAGAAACGAAACAAATTACTGTAGAAAATAACACAAACAAATGGAAATTCTTCGAAATGTTCAGAAATAATGTTAGTGCCGAATTTCAACATAAGCGCACTTTAACATCAGACACTAAATTAGCTGGGTTTATGAAATTTTATAATAGTGTTTGGACTTTTCACGGTGAAACGCCGCATGCTACAACTGATTACTCGTCAACTTCAAATTTATCTGAAGTAGAAACTGTAATACATGTTGAGTTTTATATAATACCAAGATCACAAGAATCTAAGTGCAGTGAATACATAAATACTGGGTTACCACCAATGCAAAATACAAGGAATATAGTTCCAGTTGCACTATCATCTAGATCAGTGACTTATCAACGTGCTCAGGTTAATGAGGATATCATTATATCAAAGACATCATTA';\n",
    "count = 0\n",
    "for i in range(0, len(DNA)):\n",
    "    if(DNA[i]!=''):\n",
    "        count=count+1\n",
    "print('The total number of characters in this DNA string:' + str(count));"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "retained-split",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Characters and their corresponding frequencies\n",
      "C-101\n",
      "T-173\n",
      "0-272\n",
      "G-93\n",
      "A-221\n",
      "0-583\n",
      "0-582\n",
      "0-581\n",
      "0-580\n",
      "0-579\n",
      "0-578\n",
      "0-577\n",
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      "0-575\n",
      "0-574\n",
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      "0-569\n",
      "0-568\n",
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      "0-6\n",
      "0-5\n",
      "0-4\n",
      "0-3\n",
      "0-2\n",
      "0-1\n"
     ]
    }
   ],
   "source": [
    "DNA=('CTCGATGGTCCTTATCAACCAACAAATTTTAAGCCACCAAATGATTACTGGATATTATTGAATCCAACTAATCAACAAGTTGTATTAGAGGGTACCAATAAAACTGATGTTTGGGTTGCTTTATTACTTGTTGAACCAAACGTAACCAATCAAAGTAGACAATACACATTATTTGGAGAAACGAAACAAATTACTGTAGAAAATAACACAAACAAATGGAAATTCTTCGAAATGTTCAGAAATAATGTTAGTGCCGAATTTCAACATAAGCGCACTTTAACATCAGACACTAAATTAGCTGGGTTTATGAAATTTTATAATAGTGTTTGGACTTTTCACGGTGAAACGCCGCATGCTACAACTGATTACTCGTCAACTTCAAATTTATCTGAAGTAGAAACTGTAATACATGTTGAGTTTTATATAATACCAAGATCACAAGAATCTAAGTGCAGTGAATACATAAATACTGGGTTACCACCAATGCAAAATACAAGGAATATAGTTCCAGTTGCACTATCATCTAGATCAGTGACTTATCAACGTGCTCAGGTTAATGAGGATATCATTATATCAAAGACATCATTA');\n",
    "freq=[None]*len(DNA);\n",
    "\n",
    "for i in range(0,len(DNA)):\n",
    "    freq[i]=1;\n",
    "    for j in range(i+1,len(DNA)):\n",
    "        if(DNA[i]==DNA[j]):\n",
    "            freq[i]=freq[i] + 1;\n",
    "            DNA=DNA[:j]+'0'+DNA[j+1:]\n",
    "    \n",
    "print('Characters and their corresponding frequencies');\n",
    "for i in range(0,len(freq)):\n",
    "    if(DNA[i]!=''and DNA[i]!=0):\n",
    "        print(DNA[i]+'-'+str(freq[i]));\n",
    "#PS: I do not know why the number zero is included\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "found-destiny",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of times ATG appears is 4\n"
     ]
    }
   ],
   "source": [
    "#The number of 'ATG' motifs\n",
    "DNA='CTCGATGGTCCTTATCAACCAACAAATTTTAAGCCACCAAATGATTACTGGATATTATTGAATCCAACTAATCAACAAGTTGTATTAGAGGGTACCAATAAAACTGATGTTTGGGTTGCTTTATTACTTGTTGAACCAAACGTAACCAATCAAAGTAGACAATACACATTATTTGGAGAAACGAAACAAATTACTGTAGAAAATAACACAAACAAATGGAAATTCTTCGAAATGTTCAGAAATAATGTTAGTGCCGAATTTCAACATAAGCGCACTTTAACATCAGACACTAAATTAGCTGGGTTTATGAAATTTTATAATAGTGTTTGGACTTTTCACGGTGAAACGCCGCATGCTACAACTGATTACTCGTCAACTTCAAATTTATCTGAAGTAGAAACTGTAATACATGTTGAGTTTTATATAATACCAAGATCACAAGAATCTAAGTGCAGTGAATACATAAATACTGGGTTACCACCAATGCAAAATACAAGGAATATAGTTCCAGTTGCACTATCATCTAGATCAGTGACTTATCAACGTGCTCAGGTTAATGAGGATATCATTATATCAAAGACATCATTA';\n",
    "print('The number of times ATG appears is', DNA.find('ATG'))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "id": "amended-karaoke",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The length of the sequence is 552 nucleotides\n",
      "Minimum occuring character:0\n",
      "Maximum occuring character:A\n"
     ]
    }
   ],
   "source": [
    "#Repeated letter and length of the repeating region\n",
    "print('The length of the sequence is %i' %len(DNA),'nucleotides')\n",
    "DNA=\"TGGAGTCATGGGGAAGTGAATGATTCAACAACGATAGAACCAGTACTCGATGGTCCTTATCAACCAACAAATTTTAAGCCACCAAACGATTATTGGATATTATTGAATCCAACTAATCAACAAGTCGTATTAGAGGGTACCAATAAAACTGATATTTGGGTTGCTTTATTACTTGTTGAACCAAACGTAACCAATCAAAGTAGACAATACACATTATTTGGAGAAACAAAACAAATTACTGTAGAAAATAACACAAGCAAATGGAAATTCTTCGAAATGTTCAGAAGTAGTGTTAATGCCGAGTTTCAACATAAGCGCACTCTAACATCAGACACTAAGTTAGCTGGGTTTATGAAATTTTATAATAGTGTTTGGACTTTCCACGGTGAAACGCCGTATGCTACAACTGATTACTCGTCAACTTCAAATTTATCTGAAGTAGAAACTGTAATACATGTTGAGTTTTATATAATACCAAGATCACAAGAATCTAAGTGTAGTGAATATATAAATACTGGGTTACCACCAATGCAGAATACAAGGAATATAGTT\";\n",
    "freq=[None]*len(DNA);\n",
    "minChar=DNA[0];\n",
    "maxChar=DNA[0];\n",
    "for i in range(0, len(DNA)):\n",
    "    freq[i]=1;\n",
    "    for j in range(i+1,len(DNA)):\n",
    "        if(DNA[i]==DNA[j] and DNA[i]!=''and DNA[i]!='0'):\n",
    "            freq[i]=freq[i]+1;\n",
    "            DNA=DNA[:j]+'0'+DNA[j+1:];\n",
    "min=max=freq[0];\n",
    "for i in range(0,len(freq)):\n",
    "    if(min>freq[i] and freq[i]!='0'):\n",
    "        min=freq[i];\n",
    "        minChar=DNA[i];\n",
    "    if(max<freq[i]):\n",
    "            max=freq[i];\n",
    "            maxChar=DNA[i];\n",
    "print('Minimum occuring character:'+minChar);\n",
    "print('Maximum occuring character:'+maxChar);\n",
    "                \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "floating-joyce",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Bash Script\n",
    "echo hello.sh'\n",
    "input('What is your name?')\n",
    "print('Hello',input('What is your name?.'))\n",
    "How are you?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "curious-gambling",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sequence1.fasta:3435\n"
     ]
    }
   ],
   "source": [
    "my_file = open(\"/home/toluwani/FASTA files/sequence1.fasta\")\n",
    "\n",
    "# read the contents\n",
    "my_sequence1 = my_file.read()\n",
    "\n",
    "# calculate the length\n",
    "sequence1_length = len(my_sequence1)\n",
    "\n",
    "# print the output\n",
    "print(\"sequence1.fasta:\" + str(sequence1_length))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "fresh-reviewer",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sequence2.fasta:4386\n"
     ]
    }
   ],
   "source": [
    "my_file = open(\"/home/toluwani/FASTA files/sequence2.fasta\")\n",
    "\n",
    "# read the contents\n",
    "my_sequence2 = my_file.read()\n",
    "\n",
    "# calculate the length\n",
    "sequence2_length = len(my_sequence2)\n",
    "\n",
    "# print the output\n",
    "print(\"sequence2.fasta:\" + str(sequence2_length))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "floating-arrow",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sequence3.fasta:36005\n"
     ]
    }
   ],
   "source": [
    "my_file = open(\"/home/toluwani/FASTA files/sequence3.fasta\")\n",
    "\n",
    "# read the contents\n",
    "my_sequence3 = my_file.read()\n",
    "\n",
    "# calculate the length\n",
    "sequence3_length = len(my_sequence3)\n",
    "\n",
    "# print the output\n",
    "print(\"sequence3.fasta:\" + str(sequence3_length))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "subject-pension",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sequence4.fasta:5927\n"
     ]
    }
   ],
   "source": [
    "my_file = open(\"/home/toluwani/FASTA files/sequence4.fasta\")\n",
    "\n",
    "# read the contents\n",
    "my_sequence4 = my_file.read()\n",
    "\n",
    "# calculate the length\n",
    "sequence4_length = len(my_sequence4)\n",
    "\n",
    "# print the output\n",
    "print(\"sequence4.fasta:\" + str(sequence4_length))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "conservative-broadway",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "$header\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "8"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "approved-mainland",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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