004_CG_InvertedIndex2.json

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 "metadata": {
  "name": "004_CG_InvertedIndex2"
 },
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 "nbformat_minor": 0,
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  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Let's make a class that implements an inverted (substring) index where the map data\n",
      "# structure is a sorted list of (substring, offset) pairs.  Query w/ binary search.\n",
      "\n",
      "import sys\n",
      "import bisect # for binary search\n",
      "\n",
      "class IndexSorted(object):\n",
      "    \n",
      "    def __init__(self, t, ln, ival):\n",
      "        \"\"\" Create index, extracting substrings of length 'ln' \"\"\"\n",
      "        self.t = t\n",
      "        self.ln = ln\n",
      "        self.ival = ival\n",
      "        self.index = []\n",
      "        for i in xrange(0, len(t)-ln+1):\n",
      "            self.index.append((t[i:i+ln], i)) # add <substr, offset> pair\n",
      "        self.index.sort() # sort pairs\n",
      "    \n",
      "    def query(self, p):\n",
      "        \"\"\" Return candidate alignments for p \"\"\"\n",
      "        st = bisect.bisect_left(self.index, (p[:self.ln], -1)) # binary search\n",
      "        en = bisect.bisect_right(self.index, (p[:self.ln], sys.maxint)) # binary search\n",
      "        hits = self.index[st:en] # this range of elements corresponds to the hits\n",
      "        return [ h[1] for h in hits ] # return just the offsets"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index = IndexSorted('CGTGCCTACTTACTTACAT', 5, 4)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index.query('CTTACTTA') # index: give us hints on where to look for this pattern"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 3,
       "text": [
        "[8, 12]"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index.query('TTTTTTTT') # index: give us hints on where to look for this pattern"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 4,
       "text": [
        "[]"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# Now let's make a similar class but using a Python dictionary instead of a sorted\n",
      "# list.  A Python dictionary is basically a hash table.\n",
      "\n",
      "class IndexHash(object):\n",
      "    \n",
      "    def __init__(self, t, ln, ival):\n",
      "        \"\"\" Create index, extracting substrings of length 'ln' \"\"\"\n",
      "        self.t = t\n",
      "        self.ln = ln\n",
      "        self.ival = ival\n",
      "        self.index = {}\n",
      "        for i in xrange(0, len(t)-ln+1):\n",
      "            substr = t[i:i+ln]\n",
      "            if substr in self.index:\n",
      "                self.index[substr].append(i) # substring already in dictionary\n",
      "            else:\n",
      "                self.index[substr] = [i] # add to dictionary\n",
      "    \n",
      "    def query(self, p):\n",
      "        \"\"\" Return candidate alignments for p \"\"\"\n",
      "        return self.index.get(p[:self.ln], [])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index2 = IndexHash('CGTGCCTACTTACTTACAT', 5, 4)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index2.query('CTTACTTA') # index: give us hints on where to look for this pattern"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 11,
       "text": [
        "[8, 12]"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index2.query('TTTTTTTT') # index: give us hints on where to look for this pattern "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 12,
       "text": [
        "[]"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    }
   ],
   "metadata": {}
  }
 ]
}