4.01_ShortestCommonSuperstring.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": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'ACGGATGAGCGAGCGGA'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "scs(['ACGGATGAGC', 'GAGCGGA', 'GAGCGAG'])"
   ]
  }
 ],
 "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": "2.7.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}