homework-4.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def overlap(a, b, min_length=3):\n",
    "    \"\"\" Return length of longest suffix of 'a' matching\n",
    "        a prefix of 'b' that is at least 'min_length'\n",
    "        characters long.  If no such overlap exists,\n",
    "        return 0. \"\"\"\n",
    "    start = 0  # start all the way at the left\n",
    "    while True:\n",
    "        start = a.find(b[:min_length], start)  # look for b's prefix in a\n",
    "        if start == -1:  # no more occurrences to right\n",
    "            return 0\n",
    "        # found occurrence; check for full suffix/prefix match\n",
    "        if b.startswith(a[start:]):\n",
    "            return len(a)-start\n",
    "        start += 1  # move just past previous match"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import itertools\n",
    "\n",
    "def scs(ss):\n",
    "    \"\"\" Returns shortest common superstring of given strings,\n",
    "        assuming no string is a strict substring of another \"\"\"\n",
    "    shortest_sup = None\n",
    "    for ssperm in itertools.permutations(ss):\n",
    "        sup = ssperm[0]\n",
    "        for i in range(len(ss)-1):\n",
    "            olen = overlap(ssperm[i], ssperm[i+1], min_length=1)\n",
    "            sup += ssperm[i+1][olen:]\n",
    "        if shortest_sup is None or len(sup) < len(shortest_sup):\n",
    "            shortest_sup = sup\n",
    "    return shortest_sup"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "11"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(scs(['CCT', 'CTT', 'TGC', 'TGG', 'GAT', 'ATT']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import itertools\n",
    "\n",
    "def scs_with_counts(ss):\n",
    "    \"\"\" Returns shortest common superstring of given strings,\n",
    "        assuming no string is a strict substring of another \"\"\"\n",
    "    all_scs = []\n",
    "    shortest_sup = None\n",
    "    for ssperm in itertools.permutations(ss):\n",
    "        sup = ssperm[0]\n",
    "        for i in range(len(ss)-1):\n",
    "            olen = overlap(ssperm[i], ssperm[i+1], min_length=1)\n",
    "            sup += ssperm[i+1][olen:]\n",
    "        if shortest_sup is None or len(sup) <= len(shortest_sup):\n",
    "            shortest_sup = sup\n",
    "            all_scs.append(sup)\n",
    "    return shortest_sup,all_scs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('GATTGCCTTGG',\n",
       " ['CCTTGCTGGATT',\n",
       "  'CCTTGCGATTGG',\n",
       "  'CCTTGGATTGC',\n",
       "  'TGCCTTGGATT',\n",
       "  'TGGATTGCCTT',\n",
       "  'GATTGCCTTGG'])"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scs_with_counts(['CCT', 'CTT', 'TGC', 'TGG', 'GAT', 'ATT'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('CABCA', ['ABCAB', 'BCABC', 'CABCA'])"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scs_with_counts(['ABC', 'BCA', 'CAB'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def readFastq(filename):\n",
    "    sequences = []\n",
    "    qualities = []\n",
    "    with open(filename) as fh:\n",
    "        while True:\n",
    "            fh.readline()  # skip name line\n",
    "            seq = fh.readline().rstrip()  # read base sequence\n",
    "            fh.readline()  # skip placeholder line\n",
    "            qual = fh.readline().rstrip()  # base quality line\n",
    "            if len(seq) == 0:\n",
    "                break\n",
    "            sequences.append(seq)\n",
    "            qualities.append(qual)\n",
    "    return sequences, qualities"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "seqs, quals = readFastq('ads1_week4_reads.fq')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def overlap_graph(reads, k):\n",
    "    # Make index\n",
    "    index = defaultdict(set)\n",
    "    for read in reads:\n",
    "        for i in range(len(read) - k + 1):\n",
    "            index[read[i:i+k]].add(read)\n",
    "\n",
    "    # Make graph\n",
    "    graph = defaultdict(set)\n",
    "    for r in reads:\n",
    "        for o in index[r[-k:]]:\n",
    "            if r != o:\n",
    "                if overlap(r, o, k):\n",
    "                    graph[r].add(o)\n",
    "\n",
    "    return graph\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def pick_maximal_overlap(reads, k):\n",
    "    \"\"\" Return a pair of reads from the list with a\n",
    "        maximal suffix/prefix overlap >= k.  Returns\n",
    "        overlap length 0 if there are no such overlaps.\"\"\"\n",
    "    reada, readb = None, None\n",
    "    best_olen = 0\n",
    "\n",
    "    # Make index\n",
    "    index = defaultdict(set)\n",
    "    for read in reads:\n",
    "        for i in range(len(read) - k + 1):\n",
    "            index[read[i:i+k]].add(read)\n",
    "\n",
    "    for r in reads:\n",
    "        for o in index[r[-k:]]:\n",
    "            if r != o:\n",
    "                olen = overlap(r, o, k)\n",
    "                if olen > best_olen:\n",
    "                    reada, readb = r, o\n",
    "                    best_olen = olen\n",
    "\n",
    "    return reada, readb, best_olen"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def greedy_scs(reads, k):\n",
    "    \"\"\" Greedy shortest-common-superstring merge.\n",
    "        Repeat until no edges (overlaps of length >= k)\n",
    "        remain. \"\"\"\n",
    "    read_a, read_b, olen = pick_maximal_overlap(reads, k)\n",
    "    while olen > 0:\n",
    "        reads.remove(read_a)\n",
    "        reads.remove(read_b)\n",
    "        reads.append(read_a + read_b[olen:])\n",
    "        read_a, read_b, olen = pick_maximal_overlap(reads, k)\n",
    "    return ''.join(reads)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4633\n",
      "3723\n",
      "ACCAAACAAAGTTGGGTAAGGATAGATCAATCAATGATCATATTCTAGTACACTTAGGATTCAAGATCCTATTATCAGGGACAAGAGCAGGATTAGGGATATCCGAGATGGCCACACTTTTGAGGAGCTTAGCATTGTTCAAAAGAAACAAGGACAAACCACCCATTACATCAGGATCCGGTGGAGCCATCAGAGGAATCAAACACATTATTATAGTACCAATTCCTGGAGATTCCTCAATTACCACTCGATCCAGACTACTGGACCGGTTGGTCAGGTTAATTGGAAACCCGGATGTGAGCGGGCCCAAACTAACAGGGGCACTAATAGGTATATTATCCTTATTTGTGGAGTCTCCAGGTCAATTGATTCAGAGGATCACCGATGACCCTGACGTTAGCATCAGGCTGTTAGAGGTTGTTCAGAGTGACCAGTCACAATCTGGCCTTACCTTCGCATCAAGAGGTACCAACATGGAGGATGAGGCGGACCAATACTTTTCACATGATGATCCAAGCAGTAGTGATCAATCCAGGTCCGGATGGTTCGAGAACAAGGAAATCTCAGATATTGAAGTGCAAGACCCTGAGGGATTCAACATGATTCTGGGTACCATTCTAGCCCAGATCTGGGTCTTGCTCGCAAAGGCGGTTACGGCCCCAGACACGGCAGCTGATTCGGAGCTAAGAAGGTGGATAAAGTACACCCAACAAAGAAGGGTAGTTGGTGAATTTAGATTGGAGAGAAAATGGTTGGATGTGGTGAGGAACAGGATTGCCGAGGACCTCTCTTTACGCCGATTCATGGTGGCTCTAATCCTGGATATCAAGAGGACACCCGGGAACAAACCTAGGATTGCTGAAATGATATGTGACATTGATACATATATCGTAGAGGCAGGATTAGCCAGTTTTATCCTGACTATTAAGTTTGGGATAGAAACTATGTATCCTGCTCTTGGACTGCATGAATTTGCTGGTGAGTTATCCACACTTGAGTCCTTGATGAATCTTTACCAGCAAATGGGAGAAACTGCACCCTACATGGTAATCCTAGAGAACTCAATTCAGAACAAGTTCAGTGCAGGATCATACCCTCTGCTCTGGAGCTATGCCATGGGAGTAGGAGTGGAACTTGAAAACTCCATGGGAGGTTTGAACTTTGGTCGATCTTACTTTGATCCAGCATATTTTAGATTAGGGCAAGAGATGGTGAGGAGGTCAGCTGGAAAGGTCAGTTCCACATTGGCATCCGAACTCGGTATCACTGCCGAGGATGCAAGGCTTGTTTCAGAGATTGCAATGCATACTACTGAGGACAGGATCAGTAGAGCGGTCGGACCCAGACAAGCCCAAGTGTCATTTCTACACGGTGATCAAAGTGAGAATGAGCTACCAGGATTGGGGGGCAAGGAAGATAGGAGGGTCAAACAGGGTCGGGGAGAAGCCAGGGAGAGCTACAGAGAAACCGGGTCCAGCAGAGCAAGTGATGCGAGAGCTGCCCATCCTCCAACCAGCATGCCCCTAGACATTGACACTGCATCGGAGTCAGGCCAAGATCCGCAGGACAGTCGAAGGTCAGCTGACGCCCTGCTCAGGCTGCAAGCCATGGCAGGAATCTTGGAAGAACAAGGCTCAGACACGGACACCCCTAGGGTATACAATGACAGAGATCTTCTAGACTAGGTGCGAGAGGCCGAGGACCAGAACAACATCCGCCTACCCTCCATCATTGTTATAAAAAACTTAGGAACCAGGTCCACACAGCCGCCAGCCAACCAACCATCCACTCCCACGACTGGAGCCGATGGCAGAAGAGCAGGCACGCCATGTCAAAAACGGACTGGAATGCATCCGGGCTCTCAAGGCCGAGCCCATCGGCTCACTGGCCGTCGAGGAAGCCATGGCAGCATGGTCAGAAATATCAGACAACCCAGGACAGGACCGAGCCACCTGCAAGGAAGAGGAGGCAGGCAGTTCGGGTCTCAGCAAACCATGCCTCTCAGCAATTGGATCAACTGAAGGCGGTGCACCTCGCATCCGCGGTCAGGGATCTGGAGAAAGCGATGACGACGCTGAAACTTTGGGAATCCCCTCAAGAAATCTCCAGGCATCAAGCACTGGGTTACAGTGTTATCATGTTTATGATCACAGCGGTGAAGCGGTTAAGGGAATCCAAGATGCTGACTCTATCATGGTTCAATCAGGCCTTGATGGTGATAGCACCCTCTCAGGAGGAGACGATGAATCTGAAAACAGCGATGTGGATATTGGCGAACCTGATACCGAGGGATATGCTATCACTGACCGGGGATCTGCTCCCATCTCTATGGGGTTCAGGGCTTCTGATGTTGAAACTGCAGAAGGAGGGGAGATCCACGAGCTCCTGAAACTCCAATCCAGAGGCAACAACTTTCCGAAGCTTGGGAAAACTCTCAATGTTCCTCCGCCCCCGAACCCCAGTAGGGCCAGCACTTCCGAGACACCCATTAAAAAGGGCACAGACGCGAGATTGGCCTCATTTGGAACGGAGATCGCGTCTTTATTGACAGGTGGTGCAACCCAATGTGCTCGAAAGTCACCCTCGGAACCATCAGGGCCAGGTGCACCTGCGGGGAATGTCCCCGAGTGTGTGAGCAATGCCGCACTGATACAGGAGTGGACACCCGAATCTGGTACCACAATCTCCCCGAGATCCCAGAATAATGAAGAAGGGGGAGACTATTATGATGATGAGCTGTTCTCCGATGTCCAAGACATCAAAACAGCCTTGGCCAAAATACACGAGGATAATCAGAAGATAATCTCCAAGCTAGAATCATTGCTGTTATTGAAGGGAGAAGTTGAGTCAATTAAGAAGCAGATCAACAGGCAAAATATCAGCATATCCACCCTGGAAGGACACCTCTCAAGCATCATGATTGCCATTCCTGGACTTGGGAAGGATCCCAACGACCCCACTGCAGATGTCGAACTCAATCCCGACCTGAAACCCATCATAGGCAGAGATTCAGGCCGAGCACTGGCCGAAGTTCTCAAGAAGCCCGTTGCCAGCCGACAACTCCAGGGAATGACTAATGGACGGACCAGTTCCAGAGGACAGCTGCTGAAGGAATTTCAACTAAAGCCGATCGGGAAAAAGGTGAGCTCAGCCGTCGGGTTTGTTCCTGACACCGGCCCTGCATCACGCAGTGTAATCCGCTCCATTATAAAATCCAGCCGGCTAGAGGAGGATCGGAAGCGTTACCTGATGACTCTCCTTGATGATATCAAAGGAGCCAACGATCTTGCCAAGTTCCACCAGATGCTGATGAAGATAATAATGAAGTAGCTACAGCTCAACTTACCTGCCAACCCCATGCCAGTCGACCTAATTAGTACAACCTAAATCCATTATAAAAAACTTAGGAGCAAAGTGATTGCCTCCTAAGTTCCACAATGACAGAGATCTACGATTTCGACAAGTCGGCATGGGACATCAAAGGGTCGATCGCTCCGATACAACCTACCACCTACAGTGATGGCAGGCTGGTGCCCCAGGTCAGAGTCATAGATCCTGGTCTAGGTGATAGGAAGGATGAATGCTTTATGTACATGTTTCTGCTGGGGGTTGTTGAGGACAGCGATCCCCTAGGGCCTCCAATCGGGCGAGCATTCGGGTCCCTGCCCTTAGGTGTTGGTAGATCCACAGCAAAACCCGAGGAACTCCTCAAAGAGGCCACTGAGCTTGACATAGTTGTTAGACGTACAGCAGGGCTCAATGAAAAACTGGTGTTCTACAACAACACCCCACTAACCCTCCTCACACCTTGGAGAAAGGTCCTAACAACAGGGAGTGTCTTCAATGCAAACCAAGTGTGCAATGCGGTTAATCTAATACCGCTGGACACCCCGCAGAGGTTCCGTGTTGTTTATATGAGCATCACCCGTCTTTCGGATAACGGGTATTACACCGTTCCCAGAAGAATGCTGGAATTCAGATCGGTCAATGCAGTGGCCTTCAACCTGCTAGTGACCCTTAGGATTGACAAGGCGATTGGCCCTGGGAAGATCATCGACAATGCAGAGCAACTTCCTGAGGCAACATTTATGGTCCACATCGGGAACTTCAGGAGAAAGAAGAGTGAAGTCTACTCTGCCGATTATTGCAAAATGAAAATCGAAAAGATGGGCCTGGTTTTTGCACTTGGTGGGATAGGGGGCACCAGTCTTCACATTAGAAGCACAGGCAAAATGAGCAAGACTCTCCATGCACAACTCGGGTTCAAGAAGACCTTATGTTACCCACTGATGGATATCAATGAAGACCTTAATCGGTTACTCTGGAGGAGCAGATGCAAGATAGTAAGAATCCAGGCAGTTTTGCAGCCATCAGTTCCTCAAGAATTCCGCATTTACGACGACGTGATCATAAATGATGACCAAGGACTATTCAAAGTTCTGTAGACCGCAGTGCCCAGCAATACCCGAAAACGACCCCCCTCATAATGACAGCCAGAAGGCCCGGACAAAAAAGCCCCCTCCAGAAGACTCCACGGACCAAGCGAGAGGCCAGCCAGCAGCCGACAGCAAGTGTGGACACCAGGCGGCCCAAGCACAGAACAGCCCCGACACAAGGCCACCACCAGCCATCCCAATCTGCGTCCTCCTCGTGGGACCCCCGAGGACCAACCCCGAAGGTCGCTCCGAACACAGACCACCAACCGCATCCCCACAGCTCCCGGGAAAGGAACCCCCAGCAACTGGAAGGCCCCTCCCCCCCTCCCCCAACGCAAGAACCCCACAACCGAACCGCACAAGCGACCGAGGTGACCCAACCGCAGGCATCCGACTCCTTAGACAGATCCTCTCCCCCCGGCATACTAAACAAAACTTAGGGCCAAGGAACACACACACTCGACAGAACCCAGACCCCGGCCCGCGGCACCGCGCCCCCACCCCCCGAAAACCAGAGGGAGCCCCCAACCAAACCCGCCGGCCCCCCCGGTGCCCACAGGTAGGCACACCAACCCCCGACCAGACCCAGCACCCAGCCACCGACAATCCAAGACGGGGGGCCCCCCCCAAAAAAAGGCCCCCAGGGGCCGACAGCCAGCATCGCGAGGAAGCACACCCACCCCACACACGACCACGGCAACCGAACCAGAGTCCAGACCACCCTGGGCCACCAGCTCCCAGACTCGGCCATCACCCCGCAAAAAGGAAAGGCCACAACCCGCGCACCCCAGCCCCGATCCGGCGGGCAGCCACTCAACCCGAACCAGCACCCAAGAGCGATCCCTGGGGGACCCCCAAACCGCAAAAGACATCAGTATCCCACAGCCTCTCCAAGTCCCCCGGTCTCCTCCTCTTCTCGAAGGGACCAAAAGATCAATCCACCACATCCGACGACACTCAATTCCCCACCCCCAAAGGAGACACCGGGAATCCCAGAATCAAGACTCATCCAGTGTCCATCATGGGTCTCAAGGTGAACGTCTCTGCCATATTCATGGCAGTACTGTTAACTCTCCAAACACCCACCGGTCAAATCCATTGGGGCAATCTCTCTAAGATAGGGGTGGTAGGGATAGGAAGTGCAAGCTACAAAGTTATGACTCGTTCCAGCCATCAATCATTGGTCATAAAATTAATGCCCAATATAACTCTCCTCAATAACTGCACGAGGGTAGAGATCGCAGAATACAGGAGACTACTGAGAACAGTTTTGGAACCAATTAGAGATGCACTTAATGCAATGACCCAGAATATAAGACCGGTTCAGAGTGTAGCTTCAAGTAGGAGACACAAGAGATTTGCGGGAGTTGTCCTGGCAGGTGCGGCCCTAGGCGTTGCCACAGCTGCTCAGATAACAGCCGGCATTGCACTTCACCAGTCCATGCTGAACTCTCAAGCCATCGACAATCTGAGAGCAAGCCTGGAAACTACTAATCAGGCAATTGAGGCAATCAGACAAGCAGGGCAGGAGATGATATTGGCTGTTCAGGGTGTCCAAGACTACATCAATAATGAGCTGATACCGTCTATGAACCAACTATCTTGTGATTTAATCGGCCAGAAGCTAGGGCTCAAATTGCTCAGATACTATACAGAAATCCTGTCATTATTTGGCCCCAGCTTACGGGACCCCATATCTGCGGAGATATCCATCCAGGCTTTGAGCTATGCGCTTGGAGGAGATATCAATAAGGTATTAGAAAAGCTCGGATACAGTGGAGGTGATTTACTGGGCATCTTAGAGAGCAGAGGAATAAAGGCCCGGATAACTCACGTCGACACAGAGTCCTACTTCATTGTACTCAGTATAGCCTATCCGACGCTGTCCGAGATTAAGGGGGTGATTGTCCACCGGCTAGAGGGGGTCTCGTACAATATAGGCTCTCAAGAGTGGTATACCACTGTGCCCAAGTATGTTGCAACCCAAGGGTACCTTATCTCGAATTTTGATGAGTCATCGTGTACTTTCATGCCAGAGGGGACTGTGTGCAGCCAAAATGCCTTGTACCCGATGAGTCCTCTGCTCCAAGAATGCCTCCGGGGGTCCACCAAGTCCTGTGCTCGTACACTCGTATCCGGGTCTTTTGGGAACCGGTTCATTTTATCACAAGGGAACCTAATAGCCAATTGTGCATCAATCCTCTGCAAGTGTTACACAACAGGAACGATCATTAATCAAGACCCTGACAAGATCCTAACATACATTGCTGCCGATCACTGCCCGGTGGTCGAGGTGAACGGTGTGACCATCCAAGTCGGGAGCAGGAGGTATCCGGACGCGGTGTACCTGCACAGAATTGACCTCGGTCCTCCCATATCATTGGAGAGGTTGGACGTAGGGACAAATCTGGGGAATGCAATTGCTAAGTTGGAGGATGCCAAGGAATTGTTGGAGTCATCGGACCAGATATTGAGGAGTATGAAAGGTTTATCGAGCACTAGCATAGTTTACATCCTGATTGCAGTGTGTCTTGGAGGGTTGATAGGGATCCCCGCTTTAATATGTTGCTGCAGGGGGCGCTGTAACAAAAAGGGAGAACAAGTTGGTATGTCAAGACCAGGCCTAAAGCCTGATCTTACAGGGACATCAAAATCCTATGTAAGGTCGCTCTGATCCTCTACAACTCTTGAAACACAGATTTCCCACAAGTCTCCTCTTCGTCATCAAGCAACCACCGCATCCAGCATCAAGCCCACCTGAAATTGTCTCCGGCTTCCCTCTGGCCGAACGATATCGGTAGTTAATTAAAACTTAGGGTGCAAGATCATCCACAATGTCACCACAACGAGACCGAATAAATGCCTTCTACAAAGACAACCCACATCCTAAGGGAAGTAGGATAGTTATTAACAGAGAACATCTTATGATTGATAGACCTTATGTTTTGCTGGCTGTTCTATTCGTCATGTTTCTGAGCTTGATCGGGTTGCTAGCCATTGCAGGCATTAGACTCCATCGTGCAGCCATCTACACCGCAGAGATCCATAAGAGCCTCAGCACCAATCTAGATGTAACTAACTCGATCGAGCATCAGGTCAAGGACGTGCTGACACCACTCTTCAAGATCATTGGTGATGAAGTGGGCCTGAGGACACCTCAGAGATTCACTGACCTAGTGAAATTCATCTCTGACAAAATTAAATTCCTTAATCCGGATAGGGAGTACGACTTCAGAGATCTCACTTGGTGTATCAACCCGCCAGAGAGAATCAAATTGGATTATGATCAATACTGTGCAGATGTGGCTGCTGAAGAACTCATGAATGCATTGGTGAACTCAACTCTACTGGAGGCCAGGGCAACCAATCAGTTCCTAGCTGTCTCAAAGGGAAACTGCTCAGGGCCCACTACAATCAGAGGTCAATTCTCAAACATGTCGCTGTCCCTGTTGGACTTGTATTTAAGTCGAGGTTACAATGTGTCATCTATAGTCACTATGACATCCCAGGGAATGTACGGGGGAACTTACCTAGTGGGAAAGCCTAATCTGAGCAGTAAAGGGTCAGAGTTGTCACAACTGAGCATGCACCGAGTGTTTGAAGTAGGGGTTATCAGAAATCCGGGTTTGGGGGCTCCGGTGTTCCATATGACAAACTATTTTGAGCAACCAGTCAGTAATGATTTCAGCAACTGCATGGTGGCTTTGGGGGAGCTTAAATTCGCAGCCCTCTGTCACAGGGAAGATTCTATCACAATTCCCTATCAGGGGTCAGGGAAAGGTGTCAGCTTCCAGCTCGTCAAGCTAGGTGTCTGGAAATCCCCAACCGACATGCGATCCTGGGTCCCCCTATCAACGGATGATCCAGTGATAGATAGGCTTTACCTCTCATCTCACAGAGGTGTTATCGCTGACAATCAAGCAAAATGGGCTGTCCCGACAACACGGACAGATGACAAGTTGCGAATGGAGACATGCTTCCAGCAGGCGTGTAAGGGTAAAAACCAAGCACTCTGCGAGAATCCCGAGTGGGCACCATTGAAGGATAACAGGATTCCTTCATACGGGGTCTTGTCTGTTAATCTGAGTCTGACAGTTGAGCTTAAAATCAAAATTGCTTCAGGATTCGGGCCATTGATCACACACGGTTCAGGGATGGACCTATACAAAACCAACCACAACAATGTGTATTGGCTGACTATCCCGCCAATGAAGAACCTAGCCTTAGGTGTAATCAACACATTGGAGTGGATACCGAGATTCAAGGTTAGTCCCAACCTCTTCACTGTTCCAATCAAGGAAGCAGGCGAGGACTGCCATGCCCCAACATACCTACCTGCGGAGGTGGATGGTGATGTCAAACTCAGTTCCAATCTGGTAATTCTACCTGGTCAGGATCTCCAATATGTTTTGGCAACCTACGATACTTCCAGGGTTGAACATGCTGTGGTTTATTATGTTTACAGCCCAAGCCGCTCATTTTCTTACTTTTATCCTTTTAGGTTGCCTATAAAGGGGGTCCCAATCGAATTACAAGTGGAATGCTTCACATGGGACAAAAAACTCTGGTGCCGTCACTTCTGTGTGCTTGCGGACTCAGAATCTGGTGGACATATCACTCACTCTGGGATGGTGGGCATGGGAGTCAGCTGCACAGTCACTCGGGAAGATGGAACCAATCGCAGATAGGGCTGCCAGTGAACCGATCACATGATGTCACCCAGACATCAGGCATACCCACTAGTGTGAAATAGACATCAGAATTAAGAAAAACGTAGGGTCCAAGTGGTTTCCCGTTATGGACTCGCTATCTGTCAACCAGATCTTATACCCTGAAGTTCACCTAGATAGCCCGATAGTTACCAATAAGATAGTAGCTATCCTGGAGTATGCTCGAGTCCCTCACGCTTACAGCCTGGAGGACCCTACACTGTGTCAGAACATCAAGCACCGCCTAAAAAACGGATTCTCCAACCAAATGATTATAAACAATGTGGAAGTTGGGAATGTCATCAAGTCCAAGCTTAGGAGTTATCCGGCCCACTCTCATATTCCATATCCAAATTGTAATCAGGATTTATTTAACATAGAAGACAAAGAGTCAACAAGGAAGATCCGTGAGCTCCTAAAAAAGGGAAATTCGCTGTACTCCAAAGTCAGTGATAAGGTTTTCCAATGCCTGAGGGACACTAACTCACGGCTTGGCCTAGGCTCCGAATTGAGGGAGGACATCAAGGAGAAAATTATTAACTTGGGAGTTTACATGCACAGCTCCCAATGGTTTGAGCCCTTTCTGTTTTGGTTTACAGTCAAGACTGAGATGAGGTCAGTGATTAAATCACAAACCCATACTTGCCATAGGAGGAGACACACACCTGTATTCTTCACTGGTAGTTCAGTTGAGCTGTTAATCTCTCGTGACCTTGTTGCTATAATCAGTAAGGAGTCTCAACATGTATATTACCTGACGTTTGAACTGGTTTTGATGTATTGTGATGTCATAGAGGGGAGGTTAATGACAGAGACCGCTATGACCATTGATGCTAGGTATGCAGAACTTCTAGGAAGAGTCAGATACATGTGGAAACTGATAGATGGTTTCTTCCCTGCACTCGGGAATCCAACTTATCAAATTGTAGCCATGCTGGAGCCACTTTCACTTGCTTACCTGCAACTGAGGGATATAACAGTAGAACTCAGAGGTGCTTTCCTTAACCACTGCTTTACTGAAATACATGATGTTCTTGACCAAAACGGGTTTTCTGATGAAGGTACTTATCATGAGTTAATTGAAGCCCTAGATTACATTTTCATAACTGATGACATACATCTGACAGGGGAGATTTTCTCATTTTTCAGAAGTTTCGGCCACCCCAGACTTGAAGCAGTAACGGCTGCTGAAAATGTCAGGAAATACATGAATCAGCCTAAAGTCATTGTGTATGAGACTCTGATGAAAGGTCATGCCATATTTTGTGGAATCATAATCAACGGCTATCGTGACAGGCACGGAGGCAGTTGGCCACCCCTGACCCTCCCCCTGCATGCTGCAGACACAATCCGGAATGCTCAAGCTTCAGGTGAAGGGTTAACACATGAGCAGTGCGTTGATAACTGGAAATCATTTGCTGGAGTGAGATTTGGCTGTTTTATGCCTCTTAGCCTGGACAGTGATCTGACAATGTACCTAAAGGACAAGGCACTTGCTGCTCTCCAAAGGGAATGGGATTCAGTTTACCCGAAAGAGTTCCTGCGTTACGATCCTCCCAAGGGAACCGGGTCACGGAGGCTTGTAGATGTTTTCCTTAATGATTCGAGCTTTGACCCATATGATATGATAATGTATGTCGTAAGTGGAGCCTACCTCCATGACCCTGAGTTCAACCTGTCTTACAGCCTGAAAGAAAAGGAGATCAAGGAAACAGGTAGACTTTTCGCTAAAATGACTTACAAAATGAGGGCATGCCAAGTGATCGCTGAAAATCTAATCTCAAACGGGATTGGCAAGTATTTTAAGGACAATGGGATGGCCAAGGATGAGCACGATTTGACTAAGGCACTCCACACTCTGGCTGTCTCAGGAGTCCCCAAAGATCTCAAAGAAAGTCACAGGGGGGGGCCAGTCTTAAAAACCTACTCCCGAAGCCCAGTCCACACAAGTACCAGGAACGTTAAAGCAGAAAAAGGGTTTGTAGGATTCCCTCATGTAATTCGGCAGAATCAAGACACTGATCATCCGGAGAATATAGAAACCTACGAGACAGTCAGCGCATTTATCACGACTGATCTCAAGAAGTACTGCCTTAATTGGAGATATGAGACCATCAGCTTATTTGCACAGAGGCTAAATGAGATTTACGGATTACCCTCATTTTTTCAGTGGCTGCATAAGAGGCTTGAAACCTCTGTCCTCTATGTAAGTGACCCTCATTGCCCCCCCGACCTTGACGCCCATGTCCCGTTATGCAAAGTCCCCAATGACCAAATCTTCATCAAGTACCCTATGGGAGGTATAGAAGGGTATTGTCAGAAGCTGTGGACCATCAGCACCATTCCCTACTTATACCTGGCTGCTTATGAGAGCGGGGTAAGGATTGCTTCGTTAGTGCAAGGGGACAATCAGACCATAGCCGTAACAAAAAGGGTACCCAGCACATGGCCTTACAACCTTAAGAAACGGGAAGCTGCTAGAGTAACTAGAGATTACTTTGTAATTCTTAGGCAAAGGCTACATGACATTGGCCATCACCTCAAGGCAAATGAGACAATTGTTTCATCACATTTTTTTGTCTATTCAAAAGGAATATATTATGATGGGCTACTTGTGTCCCAATCACTCAAGAGCATCGCAAGATGTGTATTCTGGTCAGAGACTATAGTTGATGAAACAAGGGCAGCATGCAGTAATATTGCTACAACAATGGCTAAAAGCATCGAGAGAGGTTATGACCGTTATCTTGCATATTCCCTGAACGTCCTAAAAGTGATACAGCAAATTTTGATCTCTCTTGGCTTCACAATCAATTCAACCATGACCCGAGATGTAGTCATACCCCTCCTCACAAACAACGATCTCTTAATAAGGATGGCACTGTTGCCCGCTCCTATTGGGGGGATGAATTATCTGAATATGAGCAGGCTGTTTGTCAGAAACATCGGTGATCCAGTAACATCATCAATTGCTGATCTCAAGAGAATGATTCTCGCATCACTAATGCCTGAAGAGACCCTCCATCAAGTAATGACACAACAACCGGGGGACTCTTCATTCCTAGACTGGGCTAGCGACCCTTACTCAGCAAATCTTGTATGCGTCCAGAGCATCACTAGACTCCTCAAGAACATAACTGCAAGGTTTGTCCTAATCCATAGTCCAAACCCAATGTTAAAAGGGTTATTCCATGATGACAGTAAAGAAGAGGACGAGAGACTGGCGGCATTCCTCATGGACAGGCATATTATAGTACCTAGGGCAGCTCATGAAATCCTGGATCATAGTGTCACAGGGGCAAGAGAGTCTATTGCAGGCATGCTAGATACCACAAAAGGCCTGATTCGAGCCAGCATGAGGAAGGGGGGGTTAACCTCTCGAGTGATAACCAGATTGTCCAATTATGACTATGAACAATTTAGAGCAGGGATGGTGCTATTGACAGGAAGAAAGAGAAATGTCCTCATTGACAAAGAGTCATGTTCAGTGCAGCTGGCTAGAGCCCTAAGAAGCCATATGTGGGCAAGACTAGCTCGAGGACGGCCTATTTACGGCCTTGAGGTCCCTGATGTACTAGAATCTATGCGAGGCCACCTTATTCGGCGTCATGAGACATGTGTCATCTGCGAGTGTGGATCAGTCAACTACGGATGGTTTTTTGTCCCCTCGGGTTGCCAACTGGATGATATTGACAAGGAAACATCATCCTTGAGAGTCCCATATATTGGTTCTACCACTGATGAGAGAACAGACATGAAGCTCGCCTTCGTAAGAGCCCCAAGTAGATCCTTGCGATCTGCCGTTAGAATAGCAACAGTGTACTCATGGGCTTACGGTGATGATGATAGCTCTTGGAACGAAGCCTGGTTGTTGGCAAGGCAAAGGGCCAATGTGAGCCTGGAGGAGCTAAGGGTGATCACTCCCATCTCGACTTCGACTAATTTAGCGCATAGGTTGAGGGATCGTAGCACTCAAGTGAAATACTCAGGTACATCCCTTGTCCGAGTGGCAAGGTATACCACAATCTCCAACGACAATCTCTCATTTGTCATATCAGATAAGAAGGTTGATACTAACTTTATATACCAACAAGGAATGCTTCTAGGGTTGGGTGTTTTAGAAACATTGTTTCGACTCGAGAAAGATACTGGATCATCTAACACGGTATTACATCTTCACGTCGAAACAGATTGTTGCGTGATCCCGATGATAGATCATCCCAGGATACCCAGCTCCCGCAAGCTAGAGCTGAGGGCAGAGCTATGTACCAACCCATTGATATATGATAATGCACCTTTAATTGACAGAGATGCAACAAGGCTATACACCCAGAGCCATAGGAGGCACCTTGTGGAATTTGTTACATGGTCCACACCCCAACTATATCACATTCTAGCTAAGTCCACAGCACTATCTATGATTGACCTGGTAACAAAATTTGAGAAGGACCATATGAATGAAATTTCAGCTCTCATAGGGGATGACGATATCAATAGTTTCATAACTGAGTTTCTGCTTATAGAGCCAAGATTATTCACCATCTACTTGGGCCAGTGTGCAGCCATCAATTGGGCATTTGATGTACATTATCATAGACCATCAGGGAAATATCAGATGGGTGAGCTGTTGTCTTCGTTCCTTTCTAGAATGAGCAAAGGAGTGTTTAAGGTGCTTGTCAATGCTCTAAGCCACCCAAAGATCTACAAGAAATTCTGGCATTGTGGTATTATAGAGCCTATCCATGGTCCTTCACTTGATGCTCAAAACTTGCACACAACTGTGTGCAACATGGTTTACACATGCTATATGACCTACCTCGACCTGTTGTTGAATGAAGAGTTAGAAGAGTTCACATTTCTTTTGTGTGAAAGCGATGAGGATGTAGTACCGGACAGATTCGACAACATCCAGGCAAAACACTTGTGTGTTCTGGCAGATTTGTACTGTCAACCAGGGACCTGCCCACCGATTCGAGGTCTAAGGCCGGTAGAGAAATGTGCAGTTCTAACCGATCATATCAAGGCAGAGGCTAGGTTATCTCCAGCAGGATCTTCGTGGAACATAAATCCAATTATTGTAGACCATTACTCATGCTCTCTGACTTATCTCCGTCGAGGATCTATCAAACAGATAAGATTGAGAGTTGATCCAGGATTCATTTTTGACGCCCTCGCTGAGGTAAATGTCAGTCAGCCAAAGGTCGGCAGCAACAACATCTCAAATATGAGCATCAAGGATTTCAGACCTCCACACGATGATGTTGCAAAATTGCTCAAAGATATCAACACAAGCAAGCACAATCTTCCCATTTCAGGGGGTAGTCTCGCCAATTATGAAATCCATGCTTTCCGCAGAATCGGGTTAAACTCATCTGCTTGCTACAAAGCTGTTGAGATATCAACATTAATTAGGAGATGCCTTGAGCCAGGGGAAGACGGCTTGTTCTTGGGTGAGGGGTCGGGTTCTATGTTGATCACTTATAAGGAGATACTAAAACTAAACAAGTGCTTCTATAATAGTGGGGTTTCCGCCAATTCTAGATCTGGTCAAAGGGAATTAGCACCCTATCCCTCCGAAGTTGGCCTTGTCGAACACAGAATGGGAGTAGGTAATATTGTCAAGGTGCTCTTTAACGGGAGGCCCGAAGTCACGTGGGTAGGCAGTATAGATTGCTTCAATTTCATAGTCAGTAATATCCCTACCTCTAGTGTGGGGTTTATCCATTCAGATATAGAGACCTTACCTAACAAAGATACTATAGAGAAGCTAGAGGAATTGGCAGCCATCTTATCGATGGCTCTACTCCTTGGCAAAATAGGATCAATACTGGTGATTAAGCTTATGCCTTTCAGCGGGGATTTTGTTCAGGGATTTATAAGCTATGTAGGGTCTCATTATAGAGAAGTGAACCTTGTCTACCCTAGGTACAGCAACTTCATATCTACTGAATCTTATTTAGTTATGACAGATCTCAAAGCTAACCGGCTAATGAATCCTGAAAAGATCAAGCAGCAGATAATTGAATCATCTGTGCGGACTTCACCTGGACTTATAGGTCACATCCTATCCATTAAGCAACTAAGCTGCATACAAGCAATTGTGGGAGGCGCAGTTAGTAGAGGTGATATCAACCCTATTCTGAAAAAACTTACACCTATAGAGCAGGTGCTGATCAGTTGCGGGTTGGCAATTAACGGACCTAAACTGTGCAAAGAATTAATCCACCATGATGTTGCCTCAGGGCAAGATGGATTGCTTAACTCTATACTCATCCTCTACAGGGAGTTGGCAAGATTCAAAGACAACCAAAGAAGTCAACAAGGGATGTTCCACGCTTACCCCGTATTGGTAAGTAGTAGGCAACGAGAACTTGTATCTAGGATCACTCGCAAATTTTGGGGGCATATTCTTCTTTACTCCGGGAACAGAAAGTTGATAAATCGGTTTATCCAGAATCTCAAGTCCGGTTATCTAGTACTAGACTTACACCAGAATATCTTCGTTAAGAATCTATCCAAGTCAGAGAAACAGATTATTATGACGGGGGGTTTAAAACGTGAGTGGGTTTTTAAGGTAACAGTCAAGGAGACCAAAGAATGGTACAAGTTAGTCGGATACAGCGCTCTGATTAAGGATTAATTGGTTGAACTCCGGAACCCTAATCCTGCCCTAGGTAGTTAGGCATTATTTGCAATATATTAAAGAAAACTTTGAAAATACGAAGTTTCTATTCCCAGCTTTGTCTGGT\n"
     ]
    }
   ],
   "source": [
    "from collections import defaultdict\n",
    "for k in range(100, 1, -1):\n",
    "        genome = greedy_scs(seqs, k)\n",
    "        if len(genome) == 15894:\n",
    "            print(genome.count('A'))\n",
    "            print(genome.count('T'))\n",
    "            print(genome)\n",
    "            break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.11"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}