Chapter_3.ipynb

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  "metadata": {
    "colab": {
      "name": "Assignment 1 Chapter 3.ipynb",
      "provenance": [],
      "collapsed_sections": [
        "-iXZ-6vaR9Lz"
      ],
      "toc_visible": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "H71heObrRXlO"
      },
      "source": [
        "#### BA3A: Generate the k-mer Composition of a String"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "lmmzKgfyQLaW",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "2d71e56d-8181-496a-b5de-76615940bfaf"
      },
      "source": [
        "\n",
        "def CompositionK(string, k):\n",
        "  kmers = set()\n",
        "  for i in range(len(string)-k+1):\n",
        "    kmers.add(string[i:i+k])\n",
        "  return kmers\n",
        "\n",
        "  \n",
        "\n",
        "# main function\n",
        "k = 5\n",
        "string = \"CAATCCAAC\"\n",
        "kmers = CompositionK(string, k)\n",
        "for kmer in kmers:\n",
        "  print(kmer)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "TCCAA\n",
            "CCAAC\n",
            "CAATC\n",
            "ATCCA\n",
            "AATCC\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "WEj-LvMPR7il"
      },
      "source": [
        "#### BA3B: Reconstruct a String from its Genome Path"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "MLBIRhtmR7rr",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 137
        },
        "outputId": "91ccb645-a183-4316-f0b2-3f61c71549f3"
      },
      "source": [
        "def GenomeReconstruction(kmers):\n",
        "  k = len(kmers[0])\n",
        "  genome = kmers[0][:k-1]\n",
        "  for kmer in kmers:\n",
        "    genome += kmer[-1]\n",
        "  return genome\n",
        "\n",
        "# main function\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Lab Task 4/rosalind_ba3b.txt', 'r') as f:\n",
        "    inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "result = GenomeReconstruction(inputLines)\n",
        "result"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'TTGTAGCCGTAACTTCGGACAGCTTCTAAGGTGTCAGCTGGAAGCAGGCACGACGTCTCCGACCCTATATCTCCCGATAACCGCCACTATGGCATGAAAGGCTTACTTAACCAGACGCCATCTCGAAACGTGATCCTTGTGAAACTTCAAGAAGTTTACGAAGCATAGGAGACCGCAGGAACTATCTCTTGGTCTCAGTGCTACAGAAGCCCAGCAGCAACGAGGACACCGGGCTTGGTCCCCCTGATTGGTTCTGTAATTTGTACACCCAAGCCTCCCTGCGCATAGTCATCGGATACTGATTGTAAAAACCTCTGGCTTTGCACCAGTCCTCTACTCTCCTGACCAAATAATACAGGAGGGTGGTCTCTTCAACGGCGCCGGCACATGTTCGAGATATATTCAATTTACCTCTTCACAATAAGGGATGAGGAAGTTGTAATTCTTAATCATCTAACCGACATTCGGCACTTCTCTTAGAACCTTATCCTAAATCGTACAGAGTCTATCGAAGTGATCTAAATATTTGGGTTTCCCCTCCGTAGAATCAAATAGGCGGATGACAAGACGGTGCGTAATACGCAACCTCCCGGGTTAGGGGATCGCTTTGCCACGCATTATGGTTGCCAACTGGAGGATGCCATACTTCCTGCATTCGTAGGACGGCCTATATAGCCACTACGACACTCGGCTGTTCTCTCCATTGAAGGCCCCCGCCGCTCCGTAATTCCGCAATACGTAGGCAACAACAACAAATGAATTCCGTTGCGTTTAAAAAGCCAACTCGAGTCTCAGCCACTGGAGCACCGTCACGCTATCACGAGATCGGTGGGATGTCTATAGTACTATGTAACATTAGATCAACACCTTGGCTGTGCCAGCACTGGACTATTCAGCTATAGTGACCAAAGCGAGTTTAGAACTTGAGGACGAGGACACGCGGGCAGGATGTAGCTGGAGCGTGGCAACGCCGCTGCAACACTTAGGCTGGCGCGCATCTACTCCGAGCGCGCCTCAGATAGCTGCCGGGTACAATACACAGGGAATGAAGATCCAATACGATTGGATTGTAACCTCCGCTAACTCATCCACTGCCCTATCAGCAAGATGGAACAATCTCCGGACTGTCGTTAGATATCTCAGCGTAGCACCAAGCCCAGTTCCCGCAGACTAGCACGTGCAGTTAAGTAAAACGCGTAGGTTCTCTTGACAACAGGCACCTACGTGGGGTCATGACTGTCCTTATGGGACCACGATGCTCATACTCCCGGCCCTAAGACATCTGTAAGGGTACGATTCGGCAATCTGGTGGTGATTGGACGGTCAAAACCCCAGTGACTGCTACAGCAGGGCGCCTGGCTCCGAACTCTTGGCCTGAGAAAGACTCAAACTGTGTCCCGTGGCGCATACGGGGGAATGTCGTCAGGCTGGGAAAATACCTCTTTCGGCCCACCAGGTGTAGTAAACCCGAAGTGCGCAGGGATCTGGGCTGTTCCGCTGTTGTGCTACGCCTTAGTGGGCTGAAGTAAATACTGATGGTTAACGTGCATGTGGGTTGAAGTTATCTAGGCGTCATCTCCTGCTTGGGGTGGAGAATTAATCCCTACGCGTTTCATACACTAAGATTAGCAGTTCACTGTACCTAGCTAAATCCGATTGACAGGATGCCAGGTCAGAAAAAGACTTTACTCACTGGCGCGACTATGCCACCGCAGGCCTTCGGGTAGGGCCCAACTCACGAGAGCGGGAGTTCGCTACAGGGTTGGGCTATTATCATCTCCTGGTGCTCACTGCAGCAAATTCGCTAACAACCGGAATATAAGTTTCCTAGGAAACTACTCGTACCCCCTGGGCAAGCGATTTATCAGTCGACTTCAGCTCTCTTGGGAGAGGAGACTAGGGCCACTGTAGTAGATATTACTAATCTCCACACACCTCTACGACGCCCAGAGCGCCCAGACAATTGTCATGTACTACGAACGACAATTAGCTGCCACCTCAATGGTGATCACCCATGCCTATCCCGGACACACCTTTGGCGCCCGAAGCGTGCACTTCGAGCTTAGTTAGATTAGAGCACTGGCCAAATGCTACCTGATATAACGTCAGAGTCAGTGACAGGGGTGAACGGGAAGCGCCCCGATTGGTAGGTACGAACAATTTCATCTCTGATTAAGAGAGCAGAGGGTAGTCGACAAGAGTCTGCCCGGGTCATGTACTCGTACGTAAGCCGACACGACTTAATGTCTGGGGCCCGCCAGAAATAGCTTCAAAGGGTAGGTTCCTGTACTTGAGAGTAGGTGAGTGGAAGAGCATTGTCAGATACAGGAGTCCACCCCACATAGCTTGACCCTCAGACCCTTAGTCAATCACCGTAGTTTAAAGTACCTTTAATAGAGGTTCTGAGGGTCGAGGCACAGCCAAGCTGCGATGAATCGTGAATGCTTCACCAAGAAATTCTCTGATCACTAGATAAGCGACCTCGGAATCACTATAAATAGCGAGTGGTATACTTTTAGAAGGACATGTATATCATGGGAAGTCATCACAATCAGCTGAACCGCAAGTTAAGCATCTCCACAGGGCGATGAGATCGATAGGTCGGCTTCACAGATATATGGACCTACCTCTACGTCCGCTATTGTGCGAATGGTTTAATGTACTTTCGCAGTTCTGGGCATAAGACAGCAGCTAATTCCGTTCCGCCCTTCTGGAGAGCGATATGCAGAAGGATTTATGGTGACGACTTCATCATGGCCTCAACTATCGAACCGAACGAAATCGAGAAACGGCTTTACTTGCTTGTTATTACTGTTGCTCGCCTCGTCCCCTGAAGTGGAGCATAGCAGGGTACGTCCTTCGCCTATCAGGAAAATCAGTCGTGTAAGACCTACCGGTCTTGTCCTTATTCTTACGGCGGCACATAAGTAACTCCTTTCCCACGGGTCATCACAAGGGCGCAGGGAATAGAAAGGACTCACGATAATGGATTAGCGTTAGGGAGTGATACGATTTTAACTCTCGTATTGCCCCCGGCAGGAGAGAAGAGCATATCCTCAGCTTTATGCCGTGGCAAGAGTCCTAAACACCAAGACGATGCCGCCCGGATATATCGCAATGTGCTTGATGCCGGCCAAAAGGTCTACGAAAGCGCTGCAAGTGTGTGCGTACCATCGGCGCACTGCTATGAAACATAATGCTTCGAGTCAGGGTTTACCGAGGAGCATTTGTGCGCGAAACATACTGGTGTTGACAAAGCAAACCGTACACTCAAAGAGGCTACTCAGCCCTTTAGATTGGTATTACACACGGCATAGGCTACGACCCCCCACAGTGCGGCGAACGTGTGCAACTTGAGGTTCGTGGATAAAATAGCACCTCGGGCCCCTTCCACTTGTCACTAAGACTGTAATCACGCTTAACATGACATTCGCCGCTCCAAAGTAGGTGCGATTACTCCCGAACGTATCGACGGCCCTGCCGCATAGCGCGGTCGGGTCAGAGTGACGTTTGAATCGCCCCAGTCGTGAGGTAAAAGCATGCAGTTAGGTTCGATTAGGCTGAGCAACTAGATGCGAGATTCCATTACCGTGAGCTCTAACCGCGGTTGGTTTGAGTCTGTTTCGCGAGGACTGATGGATTGCCCTATGCGCTCGGAGCAACCTCGGGGGGAAAGTAGGACTCGGGAACGCGTTCGTCGCGGCCTTGCATAATCCGTCACTTTCCGACTTGATCACGAGATGTGGTCGACCTCACGTTCTCCTCGGCGCTTCTCGGCTTCCGTAGCTATACATCTGATTTCATGGCAACGCGTTCCATCAGTAAACGTAGTCAATATTCTGATGCCGGATTAGGTCTCATTACGCGCCAATTCTCCCTTCATAACGCAGTTAATACGGCGCAAGGACGAAGCGGCGGCGCCCCGCGGCTTAATTACTTCTCGAATTTAATTACTATTTCCCGAAATTCTTCTGCATCTTAATTGCATGGAAGACCAACCTCTCGTACTCTATACGATGATTTCGTTCCCCTACCCGAACCATAATCGATGTGAAGGATGTTCTGATGTGCTGCTAGTAGATATAAGAAGGGTTTTAGTTTGCACCTATGGGTGGAGGTTTGACCCCTACTTCCTTGTAGTCGGTGGTTACGTTACAGGCGATTTACCTACGAGGCGACTAGATAGTCTCTCTGTCGTCGTGCAAGTAGCACGACTAACACATCAATCCCGTGTCCGCGTAACCCGGAATGATGAATTGGATACTAGAATCACCGCTCCGAGAACTGAGAACGGCATGTGATTGCAGCCCTTTTTGATCACGATTGCACGCCGCAGTAGTTCTAGCCAATGGGGAGGCCAATCCGTGTGAGGGTCCGACCGATCCGAGATAAGAGAGGTGAGAGGGTGAAGGTACAAATCCCCGGTCAAAAGCTAGATTGACTTGTGTTAGGGGTTGGAAGGGTACGAGTCTGTCCTCTACTCAATGTAGTGTTGTCGAACGCGTACTCACACACGCGTTGAGTACCAGAAAAATGATATGCATTTAACAGACGTTTTCACCTCGAAAGGCAAAGTCACTAGACTGGTCTCCGCTATCCCTGTATCAGCTGGTTTGTCGCCGACCCTGGATGGAGCGTCTTCGTTAATATGCTATCCCAGTGCGATAAGTAAGCAGGTTTTCCAAGTGCTAAACCTCCATCCCATGAATCACGCATATAGGTATGAGGGAGCTGCTCAATAGGAAACATTCGGATGGCGTAACGTTTCAGGCAATCTCGTTTTGTGCAAGAGAGGCACATCCTCCATCCTCTCTGCCATGCCGGGGACTATTGACGTAGGCCCTAAATAAGTATGAATATGTGAAATCGATATGTGGGGGAAATCAGTCACCGATTATCAGCATGACTTCGGTCCGAGAAAACACAGTCCCGCATCCCCGGGCTGCTCGCGGAAGATGTGCGCCGGTAGGCTGCAGTGTACGTGGCCGTAGTGCAGACAT'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 32
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Bkp10jJWR73S"
      },
      "source": [
        "#### BA3C: Construct the Overlap Graph of a Collection of k-mers"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "AhgMF5cdR7_b",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "8d576cba-ac6b-47d3-87c7-cf3d7c6e56d7"
      },
      "source": [
        "def getSuffix(string):\n",
        "    return string[1:len(string)]\n",
        "\n",
        "def getPrefix(string):\n",
        "    return string[0:len(string)-1]\n",
        "\n",
        "def ConstructOverlapGraph(genomelist):\n",
        "  genomelist.sort()\n",
        "  for s in genomelist:\n",
        "    for p in genomelist:\n",
        "      if getSuffix(s) == getPrefix(p):\n",
        "        print(s +\" -> \"+p)\n",
        "\n",
        "# main function\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3c.txt', 'r') as f:\n",
        "    inputLines = [line.strip() for line in f.readlines()]\n",
        "ConstructOverlapGraph(inputLines)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "AGGCA -> GGCAT\n",
            "CATGC -> ATGCG\n",
            "GCATG -> CATGC\n",
            "GGCAT -> GCATG\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Cpoi50_wR8F9"
      },
      "source": [
        "#### BA3D: Construct the De Bruijn Graph of a String"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Bk5u0oSuR8MG",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "96ba594c-04ef-4c1a-a921-d54848237f89"
      },
      "source": [
        "def getSuffix(string):\n",
        "    return string[1:len(string)]\n",
        "\n",
        "def getPrefix(string):\n",
        "    return string[0:len(string)-1]\n",
        "\n",
        "def DeBruijnK(genome, k):\n",
        "  result = {}\n",
        "  kmers = CompositionK(genome, k)\n",
        "  for kmer in kmers:\n",
        "    if getPrefix(kmer) not in result:\n",
        "      result[getPrefix(kmer)] = getSuffix(kmer)\n",
        "    else:\n",
        "      result[getPrefix(kmer)] += ',' + getSuffix(kmer)\n",
        "  return result\n",
        "\n",
        "# main function\n",
        "k = 4\n",
        "genome = \"AAGATTCTCTAC\"\n",
        "\n",
        "result = DeBruijnK(genome, k)\n",
        "\n",
        "for key, value in sorted(result.items()):\n",
        "  print(key + \" -> \" + value)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "AAG -> AGA\n",
            "AGA -> GAT\n",
            "ATT -> TTC\n",
            "CTA -> TAC\n",
            "CTC -> TCT\n",
            "GAT -> ATT\n",
            "TCT -> CTC,CTA\n",
            "TTC -> TCT\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_n-RAldzR8Ti"
      },
      "source": [
        "#### BA3E: Construct the De Bruijn Graph of a Collection of k-mers"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "TplSRZtkR8b7",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "dd32c81c-01bc-4b2a-d6b5-8cbb690199cd"
      },
      "source": [
        "def getSuffix(string):\n",
        "    return string[1:len(string)]\n",
        "\n",
        "def getPrefix(string):\n",
        "    return string[0:len(string)-1]\n",
        "\n",
        "def ConstructDeBruijn(kmers):\n",
        "  result={}\n",
        "  # if prefix of kmer is not in\n",
        "  for kmer in kmers:\n",
        "    if getPrefix(kmer) not in result:\n",
        "      result[getPrefix(kmer)] = getSuffix(kmer)  #AAGA if mydict[AAG] is not in diction\n",
        "    else:\n",
        "      result[getPrefix(kmer)] += ',' + getSuffix(kmer)\n",
        "  return result\n",
        "\n",
        "# main function\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3e.txt', 'r') as f:\n",
        "    inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "result = ConstructDeBruijn(inputLines)\n",
        "for key, value in sorted(result.items()):\n",
        "  print(str(key) + \" -> \" + str(value))"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "AGG -> GGG\n",
            "CAG -> AGG,AGG\n",
            "GAG -> AGG\n",
            "GGA -> GAG\n",
            "GGG -> GGG,GGA\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "AxOMHvvDR8jD"
      },
      "source": [
        "#### BA3F: Find an Eulerian Cycle in a Graph"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "MRT9m13wR8pt",
        "outputId": "51624afe-259e-49b7-d468-07055fd31326"
      },
      "source": [
        "from random import choice\n",
        "\n",
        "def RemoveEdge(adjList, startNode, targetNode):\n",
        "  # first remove the edge from start to target\n",
        "  adjList[startNode].remove(targetNode)\n",
        "  if not adjList[startNode]: # if there is not any associated value with startNode \n",
        "    del adjList[startNode] # delete it from list\n",
        "  return adjList\n",
        "\n",
        "def FindEuerianCycle(adjList):\n",
        "  # step 1: form a cycle Cycle by randomly walking in Graph (don't visit the same edge twice!)\n",
        "  \n",
        "  # randomly picking node and corresponding edges\n",
        "  startNode, edges = choice(list(adjList.items()))\n",
        "\n",
        "  # randomly picking one of the target nodes from edgelist\n",
        "  targetNode = choice(edges)\n",
        "\n",
        "  # as we have visited one edge, we can remove it from our adjList\n",
        "  adjList = RemoveEdge(adjList, startNode, targetNode) \n",
        "\n",
        "  # our Cycle\n",
        "  cycle = [startNode, targetNode]\n",
        "  \n",
        "  # making target node the current node from where we will continue the traversal\n",
        "  currentNode = targetNode\n",
        "\n",
        "  while currentNode != startNode:\n",
        "    # find current node edges\n",
        "    edges = adjList[currentNode]\n",
        "\n",
        "    # picking a target node randomly\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    # now again we have visited currentNode -> targetNode, so we can remove this edge\n",
        "    adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "\n",
        "    # updating currentNode\n",
        "    currentNode = targetNode\n",
        "\n",
        "    # appending new node into cycle\n",
        "    cycle.append(currentNode)\n",
        "  \n",
        "  # now we have finished step 1. Our all adjList have to be removed. \n",
        "  # now we need to check for any unexpected edges\n",
        "  # if any, then do the same process starting from unexpected edges\n",
        "  # otherwise return the cycle\n",
        "  while adjList:\n",
        "    \n",
        "    # checking if any node in cycle exist in adjList, storing them into potentialStarts\n",
        "    potentiaStarts = [(idx, node) for idx, node in enumerate(cycle) if node in adjList]\n",
        "        \n",
        "    # choosing randomly a startpoint\n",
        "    idx, newStart = choice(potentiaStarts)\n",
        "\n",
        "    # forming new cycle starting from new start and then randomly walking\n",
        "    newCycle = cycle[idx:] + cycle[1:idx+1]\n",
        "\n",
        "    edges = adjList[newStart]\n",
        "    \n",
        "    # selecting new target node\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    adjList = RemoveEdge(adjList, newStart, targetNode)\n",
        "\n",
        "    currentNode = targetNode\n",
        "    newCycle.append(currentNode)\n",
        "\n",
        "    # starting randomly traversal until currentNode != newStart\n",
        "    while currentNode != newStart:\n",
        "      edges = adjList[currentNode]\n",
        "      targetNode = choice(edges)\n",
        "      adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "      currentNode = targetNode\n",
        "      newCycle.append(currentNode)\n",
        "    cycle = newCycle\n",
        "\n",
        "  return cycle\n",
        "\n",
        "def ParseAdjList(adj_list_text):\n",
        "  adjList = {}\n",
        "  for line in inputLines:\n",
        "    # split ->\n",
        "    temp = line.split(' -> ')\n",
        "    adjList[temp[0]] = temp[1].split(',')\n",
        "  return adjList\n",
        "\n",
        "# main function\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3f.txt', 'r') as f:\n",
        "    inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "\n",
        "adjList = ParseAdjList(inputLines)\n",
        "print(adjList)\n",
        "print(\"->\".join(FindEuerianCycle(adjList)))"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "{'0': ['1', '361', '461', '526', '6', '7'], '1': ['1158', '2'], '10': ['12', '22', '56'], '100': ['102', '1079', '167', '347'], '1000': ['1002', '1192', '1746', '1856'], '1001': ['1823', '547'], '1002': ['1001'], '1003': ['107'], '1004': ['1005', '2137'], '1005': ['1003'], '1006': ['602'], '1007': ['1008'], '1008': ['1006', '1060'], '1009': ['1011'], '101': ['100'], '1010': ['2170', '561'], '1011': ['1010', '1544'], '1012': ['1014'], '1013': ['1012', '1311'], '1014': ['932'], '1015': ['1188', '324'], '1016': ['1015'], '1017': ['1016'], '1018': ['1020'], '1019': ['1018', '1769'], '102': ['202', '25', '369'], '1020': ['614'], '1021': ['1022'], '1022': ['956'], '1023': ['1021'], '1024': ['1026'], '1025': ['389'], '1026': ['1025'], '1027': ['1028'], '1028': ['176', '2267'], '1029': ['1027'], '103': ['104'], '1030': ['244'], '1031': ['1032'], '1032': ['1030'], '1033': ['551'], '1034': ['1033', '1285'], '1035': ['1034', '2560'], '1036': ['323'], '1037': ['1038'], '1038': ['1036', '1230'], '1039': ['1040'], '104': ['1565', '256', '2751', '56'], '1040': ['1041'], '1041': ['117'], '1042': ['1044'], '1043': ['394'], '1044': ['1043', '1604', '2619'], '1045': ['59'], '1046': ['1045', '2629'], '1047': ['1046', '1742'], '1048': ['1050'], '1049': ['687'], '105': ['103', '1127'], '1050': ['1049'], '1051': ['1052'], '1052': ['1053', '2173', '2662'], '1053': ['232'], '1054': ['539'], '1055': ['1056', '1367'], '1056': ['1054'], '1057': ['1059'], '1058': ['1057'], '1059': ['1612', '329'], '106': ['107', '131', '262'], '1060': ['1062'], '1061': ['1008', '1284'], '1062': ['1061'], '1063': ['1065'], '1064': ['1063'], '1065': ['2058', '494'], '1066': ['1068'], '1067': ['1066'], '1068': ['853'], '1069': ['460'], '107': ['1004', '108'], '1070': ['1069', '1105'], '1071': ['1070', '2037'], '1072': ['1073'], '1073': ['1074'], '1074': ['867'], '1075': ['1076'], '1076': ['1077'], '1077': ['661'], '1078': ['1080'], '1079': ['1078'], '108': ['1796', '47'], '1080': ['100'], 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['1259'], '1261': ['1262'], '1262': ['1263'], '1263': ['658'], '1264': ['1265'], '1265': ['2063', '249'], '1266': ['1264'], '1267': ['1268'], '1268': ['661'], '1269': ['1267'], '127': ['61'], '1270': ['1271'], '1271': ['698'], '1272': ['1270'], '1273': ['1274'], '1274': ['1275'], '1275': ['1414', '2252', '756'], '1276': ['1277'], '1277': ['53'], '1278': ['1276'], '1279': ['965'], '128': ['129', '1699', '273', '706'], '1280': ['1281'], '1281': ['1279', '1504'], '1282': ['1061'], '1283': ['1282', '2110'], '1284': ['1283'], '1285': ['1286', '1987'], '1286': ['1287'], '1287': ['1034'], '1288': ['2447', '497'], '1289': ['1288'], '129': ['127'], '1290': ['1289'], '1291': ['1292', '2279'], '1292': ['2900', '93'], '1293': ['1291'], '1294': ['985'], '1295': ['1296', '1851'], '1296': ['1294'], '1297': ['2498', '713'], '1298': ['1297'], '1299': ['1298'], '13': ['15', '2389', '422', '48'], '130': ['132'], '1300': ['1301'], '1301': ['1302'], '1302': ['854'], '1303': ['1305'], '1304': ['848'], 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['1485'], '1485': ['1483'], '1486': ['1488'], '1487': ['1486', '1933'], '1488': ['889'], '1489': ['1490', '2952'], '149': ['150', '499'], '1490': ['27'], '1491': ['1489', '1536'], '1492': ['1493', '1531'], '1493': ['743'], '1494': ['1492'], '1495': ['1497'], '1496': ['1495', '1688'], '1497': ['1471'], '1498': ['1500', '2505'], '1499': ['830'], '15': ['126', '33', '6'], '150': ['148', '642', '895'], '1500': ['1499'], '1501': ['451'], '1502': ['1501'], '1503': ['1502'], '1504': ['1506'], '1505': ['1281'], '1506': ['1505'], '1507': ['25'], '1508': ['1507', '2972'], '1509': ['1508'], '151': ['152'], '1510': ['1512'], '1511': ['2888', '559'], '1512': ['1511'], '1513': ['90'], '1514': ['1515'], '1515': ['1513'], '1516': ['67'], '1517': ['1518'], '1518': ['1516'], '1519': ['1521', '2318'], '152': ['153', '1530', '1696'], '1520': ['1519'], '1521': ['420'], '1522': ['1524'], '1523': ['1522', '1840'], '1524': ['1894', '2072', '221'], '1525': ['1526'], '1526': ['1527', '2142'], '1527': ['122'], 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['1571'], '1571': ['899'], '1572': ['1570'], '1573': ['1574'], '1574': ['1575'], '1575': ['995'], '1576': ['175'], '1577': ['1578'], '1578': ['1576'], '1579': ['931'], '158': ['157', '170'], '1580': ['1581'], '1581': ['1579'], '1582': ['1583'], '1583': ['1584', '2379', '2441'], '1584': ['93'], '1585': ['1587'], '1586': ['1585', '2796'], '1587': ['742'], '1588': ['2084', '965'], '1589': ['1588'], '159': ['158', '618'], '1590': ['1589'], '1591': ['1433', '1722', '2143'], '1592': ['1591'], '1593': ['1592'], '1594': ['1596'], '1595': ['1594'], '1596': ['643'], '1597': ['530'], '1598': ['1597'], '1599': ['1598'], '16': ['17', '457', '58', '609'], '160': ['162', '288'], '1600': ['1602'], '1601': ['1308'], '1602': ['1601', '1658'], '1603': ['1605'], '1604': ['1603'], '1605': ['1044'], '1606': ['1607'], '1607': ['1608'], '1608': ['2043', '289', '3000'], '1609': ['1611'], '161': ['160'], '1610': ['364'], '1611': ['1610'], '1612': ['1613'], '1613': ['1614'], '1614': ['1059'], '1615': ['1616'], 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['1841'], '1894': ['1895'], '1895': ['1896', '2940'], '1896': ['1524'], '1897': ['1898'], '1898': ['900'], '1899': ['1897'], '19': ['20', '2044', '354'], '190': ['1826', '191'], '1900': ['1902'], '1901': ['1900'], '1902': ['429'], '1903': ['1904'], '1904': ['209'], '1905': ['1903', '2778'], '1906': ['692'], '1907': ['1906', '2385'], '1908': ['1907', '2367'], '1909': ['1910'], '191': ['192'], '1910': ['444'], '1911': ['1909'], '1912': ['1382'], '1913': ['1912'], '1914': ['1913'], '1915': ['1417'], '1916': ['1915'], '1917': ['1916', '1922'], '1918': ['1919'], '1919': ['1920'], '192': ['157'], '1920': ['869'], '1921': ['1923'], '1922': ['1921'], '1923': ['1917'], '1924': ['94'], '1925': ['1924'], '1926': ['1925', '2136'], '1927': ['410'], '1928': ['1929'], '1929': ['1927'], '193': ['1984', '83'], '1930': ['1931'], '1931': ['1932'], '1932': ['195', '2018'], '1933': ['1935'], '1934': ['1487', '2922'], '1935': ['1934'], '1936': ['1697', '2291'], '1937': ['1936'], '1938': ['1937', '2737'], '1939': ['533'], '194': ['193'], '1940': ['1939'], '1941': ['1940'], '1942': ['1205'], '1943': ['1942'], '1944': ['1943'], '1945': ['591'], '1946': ['1947'], '1947': ['1945'], '1948': ['1949'], '1949': ['2168', '879'], '195': ['1930', '194', '464'], '1950': ['1948'], '1951': ['1551'], '1952': ['1953'], '1953': ['1951'], '1954': ['1714'], '1955': ['1954'], '1956': ['1955', '2891'], '1957': ['693'], '1958': ['1959'], '1959': ['1957'], '196': ['260', '2872', '44', '565'], '1960': ['1617'], '1961': ['1962', '2466'], '1962': ['1960'], '1963': ['1964'], '1964': ['1965'], '1965': ['1138'], '1966': ['276'], '1967': ['1968', '2275'], '1968': ['1966', '2189'], '1969': ['1971'], '197': ['196'], '1970': ['1969'], '1971': ['74'], '1972': ['37'], '1973': ['1974'], '1974': ['1972'], '1975': ['1977'], '1976': ['1975'], '1977': ['1765'], '1978': ['1979'], '1979': ['1714'], '198': ['197'], '1980': ['1978', '2313'], '1981': ['1983'], '1982': ['170'], '1983': ['1982'], '1984': ['1985'], '1985': ['1986'], '1986': ['193', '2272'], '1987': ['1989'], '1988': ['1285'], '1989': ['1988'], '199': ['200', '236', '2658'], '1990': ['934'], '1991': ['1992'], '1992': ['1990'], '1993': ['1994'], '1994': ['2589', '420'], '1995': ['1993'], '1996': ['1998'], '1997': ['2074', '352'], '1998': ['1997'], '1999': ['2001'], '2': ['3'], '20': ['1542', '21', '274'], '200': ['436', '69'], '2000': ['773'], '2001': ['2000'], '2002': ['2003', '2575'], '2003': ['2004'], '2004': ['1308'], '2005': ['2006'], '2006': ['69'], '2007': ['2005'], '2008': ['2010'], '2009': ['2008', '2217'], '201': ['199', '758'], '2010': ['1256'], '2011': ['1461'], '2012': ['2011'], '2013': ['2012'], '2014': ['2016'], '2015': ['2014'], '2016': ['692'], '2017': ['1932'], '2018': ['2019'], '2019': ['2017', '2596'], '202': ['203'], '2020': ['2022'], '2021': ['489'], '2022': ['2021'], '2023': ['1314'], '2024': ['2025', '2840'], '2025': ['2023'], '2026': ['2400', '823'], '2027': ['2028'], '2028': ['2026'], '2029': ['2030'], '203': ['204', 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['218'], '2170': ['2172'], '2171': ['1010'], '2172': ['2171'], '2173': ['2174'], '2174': ['2175'], '2175': ['1052'], '2176': ['2122'], '2177': ['2178'], '2178': ['2176'], '2179': ['2181'], '218': ['219'], '2180': ['155'], '2181': ['2180', '2756'], '2182': ['2183'], '2183': ['2184'], '2184': ['1721'], '2185': ['2186'], '2186': ['363'], '2187': ['2185'], '2188': ['2190'], '2189': ['2188'], '219': ['34'], '2190': ['1968'], '2191': ['2193'], '2192': ['2191', '2860'], '2193': ['249'], '2194': ['2195'], '2195': ['2196'], '2196': ['1721'], '2197': ['2198'], '2198': ['999'], '2199': ['2197'], '22': ['24', '311', '689'], '220': ['221'], '2200': ['1536'], '2201': ['2200'], '2202': ['2201', '2298'], '2203': ['1320'], '2204': ['2205'], '2205': ['2203'], '2206': ['2207'], '2207': ['238'], '2208': ['2206'], '2209': ['2210'], '221': ['1523', '222', '223'], '2210': ['2211'], '2211': ['2042'], '2212': ['2214', '2308'], '2213': ['2212'], '2214': ['1540'], '2215': ['2216'], '2216': ['2009'], '2217': 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['2312'], '2314': ['2315'], '2315': ['1708'], '2316': ['2314'], '2317': ['1519'], '2318': ['2319'], '2319': ['2317'], '232': ['1051', '229', '538'], '2320': ['2094'], '2321': ['2322'], '2322': ['2320'], '2323': ['1248'], '2324': ['2323'], '2325': ['2324'], '2326': ['2328'], '2327': ['2326'], '2328': ['2087'], '2329': ['2331'], '233': ['1691', '232'], '2330': ['2329'], '2331': ['791'], '2332': ['49'], '2333': ['2332'], '2334': ['2333'], '2335': ['2336'], '2336': ['2522', '358'], '2337': ['2335'], '2338': ['1087'], '2339': ['2340'], '234': ['233'], '2340': ['2338'], '2341': ['2343'], '2342': ['2341'], '2343': ['1213'], '2344': ['268'], '2345': ['2344'], '2346': ['2345', '2897'], '2347': ['2348'], '2348': ['2129'], '2349': ['2347'], '235': ['199'], '2350': ['2351'], '2351': ['2352'], '2352': ['878'], '2353': ['466'], '2354': ['2355'], '2355': ['2353'], '2356': ['2357'], '2357': ['387'], '2358': ['2356'], '2359': ['2360'], '236': ['237'], '2360': ['2361'], '2361': ['170'], '2362': 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        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "P5cl66_bR8wz"
      },
      "source": [
        "#### BA3G: Find an Eulerian Path in a Graph"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
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          "base_uri": "https://localhost:8080/"
        },
        "id": "BxMp9VZiE8Iq",
        "outputId": "11470675-b209-4327-adc9-f6b8b63cfc55"
      },
      "source": [
        "\n",
        "def FindEuerianPath(adjList):\n",
        "\n",
        "  # calculating digree difference i.e. out - in\n",
        "  degdiff = {}\n",
        "  for node, edges in adjList.items():\n",
        "    # storing indegree\n",
        "    if node in degdiff:\n",
        "      degdiff[node] += len(edges)\n",
        "    else:\n",
        "      degdiff[node] = len(edges)\n",
        "\n",
        "    # finding out outdegree of corresponding edges, if they exist in degdiff, that means\n",
        "    # they have indegree assigned by previous if else. otherwise they have no indegree.\n",
        "    # as #indegree is 1 in all the cases, so we can subtract 1 or assign -1\n",
        "    for edge in edges:\n",
        "      if edge in degdiff:\n",
        "        degdiff[edge] -= 1\n",
        "      else:\n",
        "        degdiff[edge] = -1\n",
        "  print(degdiff)\n",
        "  # storing endingNodes\n",
        "  for node, diff in degdiff.items():\n",
        "    if diff == -1:\n",
        "      endingNode = node\n",
        "\n",
        "  # storing startingNodes\n",
        "  for node, diff in degdiff.items():\n",
        "    if diff == 1:\n",
        "      startingNode = node\n",
        "      \n",
        "\n",
        "  # Euler path will exist iff euler cycle is exist\n",
        "  #if ending node present draw edge from ending to starting node\n",
        "  if endingNode in adjList:\n",
        "    adjList[endingNode].append(startingNode)\n",
        "  # else create a new edge from ending node to starting node\n",
        "  else:\n",
        "    adjList[endingNode] = startingNode\n",
        "  print(adjList)\n",
        "  eulerCycle = FindEuerianCycle(adjList)\n",
        "\n",
        "  # let's form eulerpath from starting node to ending node\n",
        "  # finding startingNode and endingNode index\n",
        "  idx = 0\n",
        "  while True:\n",
        "    if eulerCycle[idx] == endingNode and eulerCycle[idx+1] == startingNode:\n",
        "      break\n",
        "    idx += 1\n",
        "  eulerPath = eulerCycle[idx+1:] + eulerCycle[1:idx+1]\n",
        "  return eulerPath\n",
        "\n",
        "# main function\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3g.txt', 'r') as f:\n",
        "  inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "adjList = ParseAdjList(inputLines)\n",
        "print(\"->\".join(FindEuerianPath(adjList)))"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
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['1619'], '1992': ['1990'], '1993': ['502'], '1994': ['1993'], '1995': ['1994'], '1996': ['1997'], '1997': ['1998'], '1998': ['13'], '1999': ['2001', '2296'], '2': ['0', '278', '6'], '20': ['1', '1675'], '200': ['201'], '2000': ['681'], '2001': ['2000'], '2002': ['919'], '2003': ['2002'], '2004': ['2003'], '2005': ['2007', '2645'], '2006': ['2005'], '2007': ['1238'], '2008': ['2009'], '2009': ['1393'], '201': ['1134', '199'], '2010': ['2008'], '2011': ['2012'], '2012': ['755'], '2013': ['2011'], '2014': ['2015'], '2015': ['1720', '2762'], '2016': ['2014'], '2017': ['2018'], '2018': ['846'], '2019': ['2017'], '202': ['1542', '203', '2034', '498'], '2020': ['175'], '2021': ['2020'], '2022': ['2021'], '2023': ['2024', '2113'], '2024': ['494'], '2025': ['2023'], '2026': ['2027'], '2027': ['1374'], '2028': ['2026'], '2029': ['2031'], '203': ['198', '353'], '2030': ['2029'], '2031': ['2216', '512'], '2032': ['2033'], '2033': ['202'], '2034': ['2032'], '2035': ['1223'], '2036': ['2037'], 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>1152->1151->250->749->750->920->919->2109->2108->2107->919->2004->2003->2002->919->921->750->748->797->798->796->804->803->997->998->999->803->802->1862->1861->1863->802->796->748->250->363->362->361->2383->2385->2384->361->250->252->251->119->120->431->432->430->1279->1280->1281->430->120->500->501->499->120->72->214->216->386->387->385->2079->2078->2077->385->216->215->739->940->941->942->739->740->741->1452->1451\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "nYJizVXqR8-k"
      },
      "source": [
        "#### BA3H: Reconstruct a String from its k-mer Composition"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Ca6eKtD8R9FL"
      },
      "source": [
        "def getSuffixString(string):\n",
        "  return string[1:]\n",
        "\n",
        "def getPrefixString(string):\n",
        "  return string[:-1]\n",
        "\n",
        "def ReconstructGenomefromKmer(genomelist, k):\n",
        "  suffix = []\n",
        "  prefix = []\n",
        "  dect = {} # for storing last position\n",
        "  for genome in genomelist:\n",
        "    suffix.append(genome[1:])\n",
        "    prefix.append(genome[:-1])\n",
        "    dect[genome[:k-1]] = genome[k-1:k]\n",
        "  \n",
        "  # finding starting genome\n",
        "  for p in prefix:\n",
        "    if p not in suffix:\n",
        "      start = p\n",
        "      break\n",
        "  startgenome = start + dect[start]\n",
        "  # finding ending pos\n",
        "  for s in suffix:\n",
        "    if s not in prefix:\n",
        "      end = s\n",
        "      break\n",
        "  resultantPath = startgenome # initially\n",
        "  \n",
        "  while True:\n",
        "    suffixPortion = resultantPath[len(resultantPath)-k+1: len(resultantPath)] # detemining current path's suffix portion\n",
        "    if suffixPortion == end: # if it's equal to end then break\n",
        "      break\n",
        "    else: # else add the last char into path\n",
        "      resultantPath += dect[suffixPortion]\n",
        "  return resultantPath\n",
        "    \n",
        "\n",
        "  \n",
        "\n",
        "# main\n",
        "k = 4\n",
        "with open('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Lab Task 5/rosalind_ba3h.txt', 'r') as f:\n",
        "  genomelist = [line.strip() for line in f.readlines()]\n",
        "path = ReconstructGenomefromKmer(genomelist, k)\n",
        "path"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "-iXZ-6vaR9Lz"
      },
      "source": [
        "#### BA3I: Find a k-Universal Circular String"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "PBfPmjcyR9SC",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 35
        },
        "outputId": "fb548c64-485e-43e8-c7f0-ff88448ad21c"
      },
      "source": [
        "from random import choice\n",
        "\n",
        "def RemoveEdge(adjList, startNode, targetNode):\n",
        "  adjList[startNode].remove(targetNode)\n",
        "  if not adjList[startNode]: # if there is not any associated value with startNode \n",
        "    del adjList[startNode] # delete it from list\n",
        "  return adjList\n",
        "\n",
        "\n",
        "def FindEuerianCycle(adjList):\n",
        "  # step 1: form a cycle Cycle by randomly walking in Graph (don't visit the same edge twice!)\n",
        "  \n",
        "  # randomly picking node and corresponding edges\n",
        "  startNode, edges = choice(list(adjList.items()))\n",
        "\n",
        "  # randomly picking one of the target nodes from edgelist\n",
        "  targetNode = choice(edges)\n",
        "\n",
        "  # as we have visited one edge, we can remove it from our adjList\n",
        "  adjList = RemoveEdge(adjList, startNode, targetNode) \n",
        "\n",
        "  # our Cycle\n",
        "  cycle = [startNode, targetNode]\n",
        "  \n",
        "  # making target node the current node from where we will continue the traversal\n",
        "  currentNode = targetNode\n",
        "\n",
        "  while currentNode != startNode:\n",
        "    # find current node edges\n",
        "    edges = adjList[currentNode]\n",
        "\n",
        "    # picking a target node randomly\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    # now again we have visited currentNode -> targetNode, so we can remove this edge\n",
        "    adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "\n",
        "    # updating currentNode\n",
        "    currentNode = targetNode\n",
        "\n",
        "    # appending new node into cycle\n",
        "    cycle.append(currentNode)\n",
        "  \n",
        "  # now we have finished step 1. Our all adjList have to be removed. \n",
        "  # now we need to check for any unexpected edges\n",
        "  # if any, then do the same process starting from unexpected edges\n",
        "  # otherwise return the cycle\n",
        "  while adjList:\n",
        "    \n",
        "    # checking if any node in cycle exist in adjList, storing them into potentialStarts\n",
        "    potentiaStarts = [(idx, node) for idx, node in enumerate(cycle) if node in adjList]\n",
        "        \n",
        "    # choosing randomly a startpoint\n",
        "    idx, newStart = choice(potentiaStarts)\n",
        "\n",
        "    # forming new cycle starting from new start and then randomly walking\n",
        "    newCycle = cycle[idx:] + cycle[1:idx+1]\n",
        "\n",
        "    edges = adjList[newStart]\n",
        "    \n",
        "    # selecting new target node\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    adjList = RemoveEdge(adjList, newStart, targetNode)\n",
        "\n",
        "    currentNode = targetNode\n",
        "    newCycle.append(currentNode)\n",
        "\n",
        "    # starting randomly traversal until currentNode != newStart\n",
        "    while currentNode != newStart:\n",
        "      edges = adjList[currentNode]\n",
        "      targetNode = choice(edges)\n",
        "      adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "      currentNode = targetNode\n",
        "      newCycle.append(currentNode)\n",
        "    cycle = newCycle\n",
        "\n",
        "  return cycle\n",
        "\n",
        "def ParseAdjList(adjText):\n",
        "  adjList = {}\n",
        "  for key in adjText:\n",
        "    x = adjText[key].split(',')\n",
        "    adjList[key] = x\n",
        "  return adjList\n",
        "\n",
        "# k universal string has 3 steps:\n",
        "# S1: Generate binary kmers\n",
        "# S2: construct debruijn graph\n",
        "# s3: find euler cycle\n",
        "\n",
        "def generateBinarykmers(k):\n",
        "  kmers = []\n",
        "  for i in range(2**k):\n",
        "    kmer = str(bin(i))[2:]  #for removing 0b from starting\n",
        "    if kmer != k:\n",
        "      kmer = '0'*(k-len(kmer)) + kmer  \n",
        "\n",
        "    kmers.append(kmer) \n",
        "  return kmers\n",
        "\n",
        "def FindKUniversalString(k):\n",
        "  kmers = generateBinarykmers(k)\n",
        "  adjList_text = ConstructDeBruijn(kmers)\n",
        "  adjList = ParseAdjList(adjList_text)\n",
        "  cycle = FindEuerianCycle(adjList)\n",
        "\n",
        "  # k universal length will be 2^k-k+1\n",
        "  cycle = cycle[:len(cycle) - k + 1]\n",
        "\n",
        "  # now we will generate our final string, it will be 3 letters from 1st string and last letter for every string\n",
        "  # triming last character of first index\n",
        "  result = cycle[0][:-1]\n",
        "  for c in cycle:\n",
        "    result += c[-1]\n",
        "  return result\n",
        "\n",
        "# main function\n",
        "k = 3\n",
        "result = FindKUniversalString(k)\n",
        "result"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "application/vnd.google.colaboratory.intrinsic+json": {
              "type": "string"
            },
            "text/plain": [
              "'00101110'"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 68
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ntLEEdWMR9YU"
      },
      "source": [
        "#### BA3J: Reconstruct a String from its Paired Composition"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "-OV1W6ld51FJ"
      },
      "source": [
        "from collections import defaultdict\n",
        "from random import choice\n",
        "\n",
        "\n",
        "def deBruijn_graph_paired_reads(paired_reads):\n",
        "    adj_list = defaultdict(list)\n",
        "    for pair in paired_reads:\n",
        "        adj_list[(pair[0][:-1], pair[1][:-1])].append((pair[0][1:], pair[1][1:]))\n",
        "    return adj_list\n",
        "\n",
        "def RemoveEdge(adjList, startNode, targetNode):List)\n",
        "  print(\"targetNode\", targetNode, type(targetNode))\n",
        "  # if type(targetNode) != tuple:\n",
        "  #   targetNode = list(targetNode)\n",
        "  print(\"targetNode\", targetNode, type(targetNode))\n",
        "  adjList[startNode].remove(targetNode)\n",
        "  if not adjList[startNode]: # if there is not any associated value with startNode \n",
        "    del adjList[startNode] # delete it from list\n",
        "  return adjList\n",
        "  # first remove the edge from start to target\n",
        "  print(adj\n",
        "\n",
        "def FindEuerianCycle(adjList):\n",
        "  print(\"inside FindEulerian Cycle, adjList: \", adjList)\n",
        "  # step 1: form a cycle Cycle by randomly walking in Graph (don't visit the same edge twice!)\n",
        "  \n",
        "  # randomly picking node and corresponding edges\n",
        "  startNode, edges = choice(list(adjList.items()))\n",
        "\n",
        "  # randomly picking one of the target nodes from edgelist\n",
        "  targetNode = choice(edges)\n",
        "\n",
        "  # as we have visited one edge, we can remove it from our adjList\n",
        "  adjList = RemoveEdge(adjList, startNode, targetNode) \n",
        "\n",
        "  # our Cycle\n",
        "  cycle = [startNode, targetNode]\n",
        "  \n",
        "  # making target node the current node from where we will continue the traversal\n",
        "  currentNode = targetNode\n",
        "\n",
        "  while currentNode != startNode:\n",
        "    # find current node edges\n",
        "    edges = adjList[currentNode]\n",
        "\n",
        "    # picking a target node randomly\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    #print(adjList)\n",
        "    # now again we have visited currentNode -> targetNode, so we can remove this edge\n",
        "    adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "\n",
        "    # updating currentNode\n",
        "    currentNode = targetNode\n",
        "\n",
        "    # appending new node into cycle\n",
        "    cycle.append(currentNode)\n",
        "  \n",
        "  # now we have finished step 1. Our all adjList have to be removed. \n",
        "  # now we need to check for any unexpected edges\n",
        "  # if any, then do the same process starting from unexpected edges\n",
        "  # otherwise return the cycle\n",
        "  while adjList:\n",
        "    \n",
        "    # checking if any node in cycle exist in adjList, storing them into potentialStarts\n",
        "    potentiaStarts = [(idx, node) for idx, node in enumerate(cycle) if node in adjList]\n",
        "        \n",
        "    # choosing randomly a startpoint\n",
        "    idx, newStart = choice(potentiaStarts)\n",
        "\n",
        "    # forming new cycle starting from new start and then randomly walking\n",
        "    newCycle = cycle[idx:] + cycle[1:idx+1]\n",
        "\n",
        "    edges = adjList[newStart]\n",
        "    \n",
        "    # selecting new target node\n",
        "    targetNode = choice(edges)\n",
        "\n",
        "    adjList = RemoveEdge(adjList, newStart, targetNode)\n",
        "\n",
        "    currentNode = targetNode\n",
        "    newCycle.append(currentNode)\n",
        "\n",
        "    # starting randomly traversal until currentNode != newStart\n",
        "    while currentNode != newStart:\n",
        "      edges = adjList[currentNode]\n",
        "      targetNode = choice(edges)\n",
        "      adjList = RemoveEdge(adjList, currentNode, targetNode)\n",
        "      currentNode = targetNode\n",
        "      newCycle.append(currentNode)\n",
        "    cycle = newCycle\n",
        "\n",
        "  return cycle\n",
        "\n",
        "def FindEuerianPath(adjList):\n",
        "\n",
        "  # calculating digree difference i.e. out - in\n",
        "  degdiff = {}\n",
        "  for node, edges in adjList.items():\n",
        "    # storing indegree\n",
        "    if node in degdiff:\n",
        "      degdiff[node] += len(edges)\n",
        "    else:\n",
        "      degdiff[node] = len(edges)\n",
        "\n",
        "    # finding out outdegree of corresponding edges, if they exist in degdiff, that means\n",
        "    # they have indegree assigned by previous if else. otherwise they have no indegree.\n",
        "    # as #indegree is 1 in all the cases, so we can subtract 1 or assign -1\n",
        "    for edge in edges:\n",
        "      if edge in degdiff:\n",
        "        degdiff[edge] -= 1\n",
        "      else:\n",
        "        degdiff[edge] = -1\n",
        "  #print(degdiff)\n",
        "  # storing endingNodes\n",
        "  for node, diff in degdiff.items():\n",
        "    if diff == -1:\n",
        "      endingNode = node\n",
        "\n",
        "  # storing startingNodes\n",
        "  for node, diff in degdiff.items():\n",
        "    if diff == 1:\n",
        "      startingNode = node\n",
        "      \n",
        "\n",
        "  # Euler path will exist iff euler cycle is exist\n",
        "  #if ending node present draw edge from ending to starting node\n",
        "  if endingNode in adjList:\n",
        "    adjList[endingNode].append(startingNode)\n",
        "  # else create a new edge from ending node to starting node\n",
        "  else:\n",
        "    adjList[endingNode] = startingNode\n",
        "  #print(adjList)\n",
        "  \n",
        "  #print(\"inside eulerian path, adjlist: \", adjList)\n",
        "  \n",
        "  eulerCycle = FindEuerianCycle(adjList)\n",
        "\n",
        "  # let's form eulerpath from starting node to ending node\n",
        "  # finding startingNode and endingNode index\n",
        "  idx = 0\n",
        "  while True:\n",
        "    if eulerCycle[idx] == endingNode and eulerCycle[idx+1] == startingNode:\n",
        "      break\n",
        "    idx += 1\n",
        "  eulerPath = eulerCycle[idx+1:] + eulerCycle[1:idx+1]\n",
        "  return eulerPath\n",
        "\n",
        "def StringReconstructionFromPairReads(k, d, pairReads):\n",
        "  adjList = deBruijn_graph_paired_reads(pairReads)\n",
        "  print(\"DebruijnReadPairs adjList: \", adjList)\n",
        "\n",
        "  path = FindEuerianPath(adjList)\n",
        "  print(path)\n",
        "\n",
        "# main function\n",
        "k = 4\n",
        "d = 2\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3j.txt', 'r') as f:\n",
        "    inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "# generating reads from pair reads\n",
        "pairReads = []\n",
        "for line in inputLines:\n",
        "  pairReads.append(line.split('|'))\n",
        "#print(pairReads)\n",
        "StringReconstructionFromPairReads(k, d, pairReads)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "1nm12HFcR9yR"
      },
      "source": [
        "#### BA3L: Construct a String Spelled by a Gapped Genome Path"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "EAiDM_1FR94p",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "5492f12b-aa91-479a-a1e8-bce4f331d53b"
      },
      "source": [
        "\n",
        "\n",
        "def StringSpelledByGappedGenomePatterns(gappedPatterns, k, d):\n",
        "  prefix = suffix = ''\n",
        "  \n",
        "  # now traverse the gappedPatterns to construct prefix and suffix\n",
        "  for i, patterns in enumerate(gappedPatterns):\n",
        "    if i != len(gappedPatterns)-1:\n",
        "      prefix += patterns[0][0]\n",
        "      suffix += patterns[1][0]\n",
        "    else:\n",
        "      prefix += patterns[0]\n",
        "      suffix += patterns[1]\n",
        "  \n",
        "  # now check whether the overlap is perfect or not\n",
        "  for i in range(k+d+1, len(prefix)):\n",
        "    if prefix[i] != suffix[i-k-d-1]:\n",
        "      return \"String can't be contructed\"\n",
        "  return prefix + suffix[len(suffix)-k-d-1: ]\n",
        "\n",
        "\n",
        "# main function\n",
        "k = 50\n",
        "d = 200\n",
        "with open ('/content/drive/MyDrive/Bioinformatics Lab/Rosalind Dataset/Assignment/Chapter 3/rosalind_ba3l.txt', 'r') as f:\n",
        "  inputLines = [line.strip() for line in f.readlines()]\n",
        "\n",
        "# generating reads from pair reads\n",
        "gappedPatterns = []\n",
        "for line in inputLines:\n",
        "  gappedPatterns.append(line.split('|'))\n",
        "print(StringSpelledByGappedGenomePatterns(gappedPatterns, k-1, d))"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "TAAGCCTCCGCTTCAGCCTGGTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTCGAAATACGGCGTTTCTGCTCGAGAGTATTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGTGCTTCTGACAAGCGCGCTCCAGGAAATCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTTATCTTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGACGTGGACAAAGTTCAGTGGTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTCGATAGCCGCGAGCTTCTGAAGTGGACGGCGTTGGGCTGTGACACGCTTAGGGATCCGTGTGAGAGTCTTTACCTTGCTTGAGAATTCACCTGTAGAGTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGTCATTAGGGCCCACTCTCCTGGCCCAGTGTTTACATTACAAATGTAGTTCTAGGGCGACTGGAGTCTTGAAAGGTACGAAGGTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGGGATATTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTTGGCTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTTGGCTTGTAAGGTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTATCCTTATCCCCAACTCCGATCAGACGCCAGTCGCTTCTGATGCAAAGATACTCTACCGGCAAGTCCGAGTCGAATGGCTAACCACCGAGCTAAAAGACTAAGAGTTAACCGTATTCGGCGCATCCGTTAATAAATCACCCTGCACCTAATGCAAGTTATCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTATCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGTCAAGTCACGCATCATTTGTCATCTTCCACTCGAGAGTATACGACATTTCCAACGCAGTAGTCTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTGCTTGGGATATTTGGCTCGCGCTAAGCCGGGATCGAGAGTATACGACATTTCCAACGTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTCAGTAGTCGCTTGGGATATTTGGCTAGCAGGCCGGGGCGCGAGGAACGAATTAAATCCAGAGAATCCGACACTGTTCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTCGCCGGGCAGGGCGATCAGCTATGGTAACGGGCACCGGGCAGACATTCCAAACCAGTAATTGATACAAATAACGATGAAATAGAGAGCGCGGCGCAAACCTGACATGCAGCCCTAAGAGGTGAGAAAGGATCCAACGGCTTCCACTGTGGAGGGCTAAACCACCAGTTAGATTCCTATACATTTGATACCTCAGTAAAGGCCGTAGACTCGGTAATCAGATCGCTAGGTCGTTACTTTACTGTTGGCGCGTGGCTTGGGCTCAGATGCGTCTTCGAGAACCACACCGCTACTTGTAACCTGATCCCTAAGGCCCACAGCTAGTCCCTCACCCAGCGCCACGGGGACCGCATTGCTCACTCTTTCGCTGTTTTGGATGAGTTAAAAAATAACGCCAGGATCTAATTTTGAGGCGTCTCCACACGCTTGAGGTATTTTTGCCGGGTCAGTAGATCGAGAGTATACGACATTTCCAACGCAGTAGTCGCTTGGGATATTTGGCTATGG\n"
          ],
          "name": "stdout"
        }
      ]
    }
  ]
}