CG_ErrorCorrect.json

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  "name": ""
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  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def neighbors1mm(kmer, alpha):\n",
      "    ''' Generate all neighbors at Hamming distance 1 from kmer '''\n",
      "    neighbors = []\n",
      "    for j in xrange(len(kmer)-1, -1, -1):\n",
      "        oldc = kmer[j]\n",
      "        for c in alpha:\n",
      "            if c == oldc: continue\n",
      "            neighbors.append(kmer[:j] + c + kmer[j+1:])\n",
      "    return neighbors"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "neighbors1mm('CAT', 'ACGT')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 2,
       "text": [
        "['CAA', 'CAC', 'CAG', 'CCT', 'CGT', 'CTT', 'AAT', 'GAT', 'TAT']"
       ]
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def kmerHist(reads, k):\n",
      "    ''' Return k-mer histogram and average # k-mer occurrences '''\n",
      "    kmerhist = {}\n",
      "    for read in reads:\n",
      "        for kmer in [ read[i:i+k] for i in xrange(0, len(read)-(k-1)) ]:\n",
      "            kmerhist[kmer] = kmerhist.get(kmer, 0) + 1\n",
      "    return kmerhist"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "khist = kmerHist(['CAT' * 10], 3)\n",
      "khist"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 4,
       "text": [
        "{'ATC': 9, 'CAT': 10, 'TCA': 9}"
       ]
      }
     ],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def correct1mm(read, k, kmerhist, alpha, thresh):\n",
      "    ''' Return an error-corrected version of read.  k = k-mer length.\n",
      "        kmerhist is kmer count map.  alpha is alphabet.  thresh is\n",
      "        count threshold above which k-mer is considered correct. '''\n",
      "    # Iterate over k-mers in read\n",
      "    for i in xrange(0, len(read)-(k-1)):\n",
      "        kmer = read[i:i+k]\n",
      "        # If k-mer is infrequent...\n",
      "        if kmerhist.get(kmer, 0) <= thresh:\n",
      "            # Look for a frequent neighbor\n",
      "            for newkmer in neighbors1mm(kmer, alpha):\n",
      "                if kmerhist.get(newkmer, 0) > thresh:\n",
      "                    # Found a frequent neighbor; replace old kmer\n",
      "                    # with neighbor\n",
      "                    read = read[:i] + newkmer + read[i+k:]\n",
      "                    break\n",
      "    # Return possibly-corrected read\n",
      "    return read"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "correct1mm('CAT', 3, khist, 'ACGT', 2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 6,
       "text": [
        "'CAT'"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "correct1mm('CTT', 3, khist, 'ACGT', 2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "'CAT'"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    }
   ],
   "metadata": {}
  }
 ]
}