Rosalind.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "def count_letters(sequence: str) -> list:\n",
    "    letters = ['A', 'C', 'G', 'T']\n",
    "    counts = []\n",
    "    for character in letters:\n",
    "        count = 0\n",
    "        for i in range(len(sequence)):\n",
    "            if sequence[i] == character:\n",
    "                count += 1\n",
    "        counts.append(count)\n",
    "    return counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "278 238 238 240\n"
     ]
    }
   ],
   "source": [
    "sequence = \"AGCGGTTGGCTGCATTACTCCGGTAAATCTCGTGCGCTCTTCTTATAGCAGCCGATCGACTAGCTTGAGTACGACTGCGGATGGTTCTTGGGTCATTAAATTCCTGTGTACTGCCTATCCGGTGGGCTATACTCGTTTCACACCCAAAAATAAGACCACTCTAGTCTCGCCGGATCGCTTTAGCTACTGTAGTCACGCTAATACAGAAGACAGTCAAGTAACATGTAGGTGGAGAACCGACGACTACTAGGATCAGTCCCGACCCTCTGTCAATCCTAGGAACGCTCAAGAACCTTCAGATTATAACACCGATCTCCGGGATCTTGACCGACATGCGACCAAGAGAAAAGCCGGGACCACGACAGACGCATAAACATGGTCGCGCCGTTGTTGGAGACCCAGGCAACCTCATGCCCATAATGCTCCGCAGGGCAGGGGGGTTCCCATCACTTGCATTGGTAGAACTGCATTTATGCACATAGATTTGGATTCTAAAATGTGCTTCTAGCACGTCCGGCTTACCCTAAGTAGAAAACTTGGGATAGCGAAGGCGTTTACGAGGGGGAGATTAGAAGCCACATCCTTCATTTCGAAACTCCCATGGGCTCCAAACAAGCGCAGTGATTGCCCGACCGCCGAGGGGATATGTGTGATGCAGCAAAATCCTCAGCGGTAAAAGAACGTGGTATGTGAGTATCGCGAAGTGTGGCTAAAAAAGACCTCCGATCAAGGTATTCTCTTTATAGAGGCTAGCCAACGTTACAAAATCATACCGTACTATAACTCCATATGAGCGCTAGAAAACAGATGCTCAAGATGAGAAAATTTGTTGATACATAACTGATGCACAGGTAGCCTCTGGCCGGGAATCTTCGGGATTCAACCTCTTATTCTTATAGTGGGAGAGGTTAATTCACGTTAACAATAACAATGAAATGGTATAGTTCAGGTACTGCCCTGATCCCTCGGCTAGGCGCGAACATGCGTTTGAACT\"\n",
    "answer = count_letters(sequence)\n",
    "print(\" \".join(str(x) for x in answer))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "def replace_t_with_u(sequence: str) -> str:\n",
    "    RNA = \"\"\n",
    "    for i in range(len(sequence)):\n",
    "        if sequence[i] == 'T':\n",
    "            RNA = RNA + 'U'\n",
    "        else:\n",
    "            RNA = RNA + sequence[i]\n",
    "    return RNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AUUGGCUGAAGUGACGAGAAACUUCUAAGGACCUGCGUGAUAGUCUAGUCACUUUAUAUCGCUAGACAAUUUAGCGUGAUGGCUUGCGUGUUAAUGCACAUUACAAUGGGAAGUAAGCCCGAGACUCUCUAGGGGACCUGCGAAUAACUCUGGAUGGCUUUUUAAUCAUUUACGAUAAUUGUGUCUGAGUUACGGUGACAUAAAUAAGGACUAGUCGUGGCGCUUUCGCCUGUCCACAACCUCGGUCUGUAGAACGCAGUGAUAGUUAGCAUGGAUCCGAGUUUGCUGAUGGAAGCCUCGCACGGUAAAACCUGGGCGACGAGGGCCGGACGCGGCGUGCCCAGAUACCGAACUGCGCUAAUCUUAAGUAUUUUGCAAAGACAUAUCGAACGUUAUUCACCUCAGGCACAUGGUAAGGAAGGUCGUCGGUCACAUGGAUAGGCCUCAGAUGUUUGAGACUAAAACAUAUCGGAAUCGGGUGACCUGCCUAUCGCAGCACAGCCACGUUAUUCCAGGUCUCGUCGCGCUUUCGUGAUGUGCGGUGAACCACGAUGCAUAAUAUGUUGAGUAUUCAGGACACUUUAGGCAGUCAUUAGUACUACGGUCUUCGUGGGACUCGUCACGGGCGUGAGAUUCAACUGUCUGCAAGCGGCCCCAUUUGCUGCCACUUAAAGCUCGAGACUAGAGGAGCAUUGAUGUCAGUUCGACGACCAAACAGUAUCAGAAACGAGCUCAGCGAGUAAGCCUUUCGCUAUCAAUUGGUAUAGCGGCCCCUAUGUCAUAUCCUCUAGCAGAAUGGACGCCACUUACUUAGUUUCUGAAGUAGUGCUUCGUGCGAUGCGUCCGGGCCGGGCUACUGUCAAAGGCAAUCGGGACUGCGACCCGAUGCUUCGCGAAAGACACGGCAAGCUCCUGCGGGCUUGCGAGACGACGUGCAAACUCAGUAUAAAUGUCUGGCAGAACCAGCAA\n"
     ]
    }
   ],
   "source": [
    "seq = \"ATTGGCTGAAGTGACGAGAAACTTCTAAGGACCTGCGTGATAGTCTAGTCACTTTATATCGCTAGACAATTTAGCGTGATGGCTTGCGTGTTAATGCACATTACAATGGGAAGTAAGCCCGAGACTCTCTAGGGGACCTGCGAATAACTCTGGATGGCTTTTTAATCATTTACGATAATTGTGTCTGAGTTACGGTGACATAAATAAGGACTAGTCGTGGCGCTTTCGCCTGTCCACAACCTCGGTCTGTAGAACGCAGTGATAGTTAGCATGGATCCGAGTTTGCTGATGGAAGCCTCGCACGGTAAAACCTGGGCGACGAGGGCCGGACGCGGCGTGCCCAGATACCGAACTGCGCTAATCTTAAGTATTTTGCAAAGACATATCGAACGTTATTCACCTCAGGCACATGGTAAGGAAGGTCGTCGGTCACATGGATAGGCCTCAGATGTTTGAGACTAAAACATATCGGAATCGGGTGACCTGCCTATCGCAGCACAGCCACGTTATTCCAGGTCTCGTCGCGCTTTCGTGATGTGCGGTGAACCACGATGCATAATATGTTGAGTATTCAGGACACTTTAGGCAGTCATTAGTACTACGGTCTTCGTGGGACTCGTCACGGGCGTGAGATTCAACTGTCTGCAAGCGGCCCCATTTGCTGCCACTTAAAGCTCGAGACTAGAGGAGCATTGATGTCAGTTCGACGACCAAACAGTATCAGAAACGAGCTCAGCGAGTAAGCCTTTCGCTATCAATTGGTATAGCGGCCCCTATGTCATATCCTCTAGCAGAATGGACGCCACTTACTTAGTTTCTGAAGTAGTGCTTCGTGCGATGCGTCCGGGCCGGGCTACTGTCAAAGGCAATCGGGACTGCGACCCGATGCTTCGCGAAAGACACGGCAAGCTCCTGCGGGCTTGCGAGACGACGTGCAAACTCAGTATAAATGTCTGGCAGAACCAGCAA\"\n",
    "answer = replace_t_with_u(seq)\n",
    "print(answer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def rev_comp(sequence: str) -> str:\n",
    "    comps = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}\n",
    "    new_seq = \"\"\n",
    "    for i in range(len(sequence)):\n",
    "        new_seq = comps[sequence[i]] + new_seq\n",
    "    return new_seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ACCGGGTTTT\n"
     ]
    }
   ],
   "source": [
    "sequence = \"AAAACCCGGT\"\n",
    "answer = rev_comp(sequence)\n",
    "print(answer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GCAATGTAATGGTCTAAACTAGAAGCCACAACTACTCTATCGGTTGGGTCTTGAAGACATCTACATGCAGCGAGGCGTGCCTATCTTTAGACCACTAATCCAAATGACATATTTATTACTTCGGTCGACTTTGGGTCTCGTGACGGTGTTTATCACGTGTCTCGGGTGAAGGAAGATTTTTGCGGACCTTATCAAGGGGGATATCGTCACAGCGTCCTGGTACTATCCTAGTCATAAAGTAGCGTCAGGTGTCGTTTGCCAACTCGATATATCATACTGTACGCCCTGGAGATCGTCAGCGTCCAGTTGGTTGTGTAGGGGCAAGGGTAGTCTACTAAAACTAGTGATTTTTAGGCGTCAGGACAACCAAACCCTATGTAGTTCTATCGGCTTTGATCGCCTTCAGCCTTTGTTCGCGAAGTCACTTTCTGACCGACCCGCCTCCATAGGAATCTCACGGTCACCAAACTTGAGCAGTCAGTTAGTATATTTCGATCAAGGGTAGCGTTTGACGGCCTCTGTGCATTCTTGGTATAGGGTAGAGCTGCAGATGTCTGCGACTTAGAGAATGGAGAGATACGGCTATGTGGTTCGCAGACCTCGTTCTCCAAGCGCAACCAATTCGACTAATTGGCCGGGATTCAATGTTTTACTAAGTGTGTGGTCGGCTATCAGCAATATACGTATGCTCCCTCTATGACTTACGCCGTGTACCAAAATGTGACGGGTCTGAGGCCATATGTAGCAGAATAAGACAACACGATGGTTACGGGCGCGGGTCGAACAAACTACTCCAATTCATAGTGCCTTGAGATAGCTGCACGTAGTCATCCGCCGATAGTACCCTTTGATGGGTAGTTTCAAATTCTGTAGCGTCCACATATAAGACAACTAGCACATTATTCGTGACAATTCTCGTTCTATCGTAACTATGTGGTGTTACGTACCCAT\n"
     ]
    }
   ],
   "source": [
    "sequence = \"ATGGGTACGTAACACCACATAGTTACGATAGAACGAGAATTGTCACGAATAATGTGCTAGTTGTCTTATATGTGGACGCTACAGAATTTGAAACTACCCATCAAAGGGTACTATCGGCGGATGACTACGTGCAGCTATCTCAAGGCACTATGAATTGGAGTAGTTTGTTCGACCCGCGCCCGTAACCATCGTGTTGTCTTATTCTGCTACATATGGCCTCAGACCCGTCACATTTTGGTACACGGCGTAAGTCATAGAGGGAGCATACGTATATTGCTGATAGCCGACCACACACTTAGTAAAACATTGAATCCCGGCCAATTAGTCGAATTGGTTGCGCTTGGAGAACGAGGTCTGCGAACCACATAGCCGTATCTCTCCATTCTCTAAGTCGCAGACATCTGCAGCTCTACCCTATACCAAGAATGCACAGAGGCCGTCAAACGCTACCCTTGATCGAAATATACTAACTGACTGCTCAAGTTTGGTGACCGTGAGATTCCTATGGAGGCGGGTCGGTCAGAAAGTGACTTCGCGAACAAAGGCTGAAGGCGATCAAAGCCGATAGAACTACATAGGGTTTGGTTGTCCTGACGCCTAAAAATCACTAGTTTTAGTAGACTACCCTTGCCCCTACACAACCAACTGGACGCTGACGATCTCCAGGGCGTACAGTATGATATATCGAGTTGGCAAACGACACCTGACGCTACTTTATGACTAGGATAGTACCAGGACGCTGTGACGATATCCCCCTTGATAAGGTCCGCAAAAATCTTCCTTCACCCGAGACACGTGATAAACACCGTCACGAGACCCAAAGTCGACCGAAGTAATAAATATGTCATTTGGATTAGTGGTCTAAAGATAGGCACGCCTCGCTGCATGTAGATGTCTTCAAGACCCAACCGATAGAGTAGTTGTGGCTTCTAGTTTAGACCATTACATTGC\"\n",
    "answer = rev_comp(sequence)\n",
    "print(answer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def rabbits_after_months(n: int, k: int) -> int:\n",
    "    F_n = 0\n",
    "    F_n1 = 1\n",
    "    F_n2 = 1\n",
    "    for i in range(n-2):\n",
    "        F_n = F_n1 + (k * F_n2)\n",
    "        F_n2 = F_n1\n",
    "        F_n1 = F_n\n",
    "    return F_n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "249650241628\n"
     ]
    }
   ],
   "source": [
    "n = 33\n",
    "k = 3\n",
    "answer = rabbits_after_months(n, k)\n",
    "print(answer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_gc_content(sequence: str) -> float:\n",
    "    count = 0\n",
    "    for letter in sequence:\n",
    "        if letter == \"G\" or letter == \"C\":\n",
    "            count += 1\n",
    "    return count/len(sequence)\n",
    "\n",
    "def read_fasta(filename: str) -> dict:\n",
    "    dictionary = {}\n",
    "    temp_key = \"\"\n",
    "    temp_sequence = \"\"\n",
    "    first_time = 1\n",
    "    file = open(filename, 'r')\n",
    "    \n",
    "    for line in file:\n",
    "        line = line.rstrip()\n",
    "        if line[0] == \">\":\n",
    "            if first_time == 1:\n",
    "                first_time = 0\n",
    "                temp_key = line[1:]\n",
    "            else:\n",
    "                dictionary[temp_key] = temp_sequence\n",
    "                temp_sequence = \"\"\n",
    "                temp_key = line[1:]\n",
    "        else:\n",
    "            temp_sequence += line\n",
    "    dictionary[temp_key] = temp_sequence\n",
    "    return dictionary\n",
    "\n",
    "def process_fasta_gc(dictionary: dict) -> list:\n",
    "    gc_percents = []\n",
    "    gc_keys = []\n",
    "    for key in dictionary:\n",
    "        gc_keys.append(key)\n",
    "        gc_percents.append(get_gc_content(dictionary[key]))\n",
    "    index = gc_percents.index(max(gc_percents))\n",
    "    return gc_keys[index], gc_percents[index]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.5375\n"
     ]
    }
   ],
   "source": [
    "b = \"CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG\"\n",
    "print(get_gc_content(b))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Rosalind_8830\n",
      "51.108647450110865\n"
     ]
    }
   ],
   "source": [
    "temp_dict = read_fasta(\"data.txt\")\n",
    "print(process_fasta_gc(temp_dict)[0])\n",
    "print(process_fasta_gc(temp_dict)[1] * 100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [],
   "source": [
    "def hamming_distance(string1: str, string2: str) -> int:\n",
    "    distance = 0\n",
    "    if len(string1) != len(string2):\n",
    "        print(\"Can't compare these two strings\")\n",
    "    else:\n",
    "        for i in range(len(string1)):\n",
    "            if string1[i] != string2[i]:\n",
    "                distance += 1\n",
    "    return distance        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "483\n"
     ]
    }
   ],
   "source": [
    "a = \"GTCGGTCCTACTGGCATGAGACCACAAGCCCAAATTAAAGCATTGTTATATGTCTTACGACCATACAGTCCAACTCCAAAGCGAAGCGTAGGCACTGCTCATGCCTGGTTTACCCTGGGTCTGCCCGCGGCGGCACAGCCTGGTACAAGATTATCTCAACGCATCACGCCTCCCCCTTCTAATGGGTTACTGTCGTGCTCGTACGGTAAGTGGGAAGAGCTGCTAGCTGCGTGGCTCTGTCTCCACGTAATCTATGGCACGTTTGAATGGATTCCCCGCAATATTTGGGATTCATTGGACTCAACAACGGCCCCAAGTAGAGACTGAACTGCCTGAATACTGGGAGCTTGGCGGGGTCAATGAGCCGGACGTCATAGAGACGCACCCTTAAGTAGTGCGTTTTAATAGTATTGGGGGTCTGACAGAACCTCACAGTTAGATAACGTACGATGGTCTAAGAGACCTTAAACGCTACTAGCATCGCTCCACATACGGGAAAGGGCTGTTAACACAAAGGTGCCTCTACGCCTTGTCTGGAACTATACGTTGCTCGGTCCGGACAGAGTCTTAACTGCTGCTACATTCTAATTACTGTTGCGGTCGCACTCTTACTAGATCCCCACGGGATATAGCTTTACAAGCCCTTGCAACTATCTCCAGTGCACCGGAAATACGTAATCCGAGCCATCGATCGACAAATCTACTTAGAACTCTCCCCAAGCATAGGGTATCCTCGATTGATGCTCGGTAAAGGGCACTTAACCTAACTGAGGAAACTGTTATGGGATAGCCGTGGTCGTCTCCAACGTTTTGTCAACACATTTTTCTGGTTATAGGTGTATCGGATATAACGAGCATTTCCGGCGTCGCAAGGTGTCTTATGAGGGCGAATTGCCGATACTTCGTAAGGGTGCAGCAACGCTCTTTTACCTGACTAAACACTTTCCAGCATCGTTTATTAATTCCCGCGGCCACTTGGTTGC\"\n",
    "b = \"GGCAGCCCGCCTTGCAGGGGACTACCAGTGCAAATACACACGGTGAGAGATAACCGAATAACCGGCGGCTTCGCTCCCAAATTACTAGCATACTCTAATCGTTCCTGAAACTGGCCGGAGCGGCGCACGAGGGGACTGCCCGGTACATAGACATGTATTAACATCTCGCATCCAGATCCAGCTATTTTGTCATAGTGCGACCAAGGATAGCGGCAATAACTGTTAGCTGTCAAGTTGTGTCTCCAAGTTTATCATTACACAATTGATTAGATTTTCATATGTGGACTGGATTAGTTGATCTCCCCACAGCCCCCAAGTCGATCCGACCCTATCAGGAAACTGTGAGGTGCCCTTGGTCCTCAAGTCTGAACCCAATGGGACGGAGCCTCTAATTGTGCCTTCTACTAGTCGGGGGCTTGCGACAACGACCCGCTGGAAGGATAAGCGCGCTTGTATAACGGGGCTGAAAAGGTATCAACGTGGTTTAAACTTTTAGAATTGACTCCTAATATAAACGAGTCCTCACGTCGTTCATGTTTCCACACATGAATACGCCGTGCAAGTATCCCTTGTCCTACTACATTCTAAGTGCAGTACCGGCGACGCATGTACCCGCGAGCAGCGACCTATAACCGACCGATCCTTTGCAACCATGGACAATGAGCCGGGCCTGAGCTATCGTAATGACCCATCGACGAATCTTCCGCCTTACCGTAAGGATCTTCTGTGGTACCATACTCAATCTCTGACAAACACACATCTCTGCTCAATCAACACTGGTACGACTTCCACCTTGGACCATACTATGTCTTGTTAACACTACTATCATGGTAGACGTGAATCGAATACTTTGGTTATTCCGGGCACAGATATGACTATGGCGATGCCGTATATCAGCTACGTCCCTCGGCGATTGCTACCATGGTCTACACTAATATCCAGTCCTTTGCGTCGGCTGGTAATTGTCCATAGCGCTTGTTGAC\"\n",
    "print(hamming_distance(a, b))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "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": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}