khmer_play.ipynb

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import khmer\n",
      "import gzip\n",
      "from collections import Counter"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 38
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /nas3/gpratt/projects/encode/fastq/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/nas/nas0/gpratt/projects/encode/fastq\n"
       ]
      }
     ],
     "prompt_number": 39
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "bptm = khmer.new_ktable(15)\n",
      "file_handle = gzip.open(\"BPTM_NoIndex_L006_R1.R01_TAF15_TA1M.fastq.gz\")\n",
      "while True:\n",
      "    try:\n",
      "        name = file_handle.next()\n",
      "        seq = file_handle.next().strip()\n",
      "        plus = file_handle.next()\n",
      "        qual = file_handle.next()\n",
      "        bptm.consume(seq)\n",
      "    except Exception as e:\n",
      "        print e\n",
      "        break"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 40
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "bpth = khmer.new_ktable(15)\n",
      "file_handle = gzip.open(\"BPTH_NoIndex_L005_R1.R01_TAF15_TA1H.fastq.gz\")\n",
      "while True:\n",
      "    try:\n",
      "        name = file_handle.next()\n",
      "        seq = file_handle.next().strip()\n",
      "        plus = file_handle.next()\n",
      "        qual = file_handle.next()\n",
      "        bptm.consume(seq)\n",
      "    except Exception as e:\n",
      "        print e\n",
      "        break"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 41
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "intersected = bpth.intersect(bptm)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "distribution_bptm= Counter()\n",
      "distribution_bpth= Counter()\n",
      "distribution_intersect= Counter()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 44
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for i in xrange(0, bptm.n_entries()):\n",
      "    bptm_count = bptm.get(i)\n",
      "    bpth_count = bpth.get(i)\n",
      "    intersected_count = intersected.get(i)\n",
      "    #if bptm_count > 0 or bpth_count >0:\n",
      "    distribution_bptm[bptm_count] += 1\n",
      "    distribution_bpth[bptm_count] += 1\n",
      "    distribution_intersect[intersected_count] += 1"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 45
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "100000000. /bptm.n_entries()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 9,
       "text": [
        "0.09313225746154785"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "min(distribution), max(distribution)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 10,
       "text": [
        "(0L, 80470L)"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "x = hist(distribution, bins=100)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "display_data",
       "png": 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bN27cuH2PW0JCQnuZ/sG6qh09e/aUdP0TPwMGDNDWrVv18ssvt1njcrlUXFysZ599VhUV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\nQmCC\n",
       "text": [
        "<matplotlib.figure.Figure at 0x2217b610>"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Counter(distribution_bptm).most_common(10)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 17,
       "text": [
        "[(1L, 21595),\n",
        " (2L, 4018),\n",
        " (3L, 1819),\n",
        " (4L, 1187),\n",
        " (5L, 950),\n",
        " (6L, 736),\n",
        " (7L, 536),\n",
        " (8L, 506),\n",
        " (10L, 345),\n",
        " (9L, 323)]"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Counter(distribution_bpth).most_common(10)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 18,
       "text": [
        "[(1L, 21595),\n",
        " (2L, 4018),\n",
        " (3L, 1819),\n",
        " (4L, 1187),\n",
        " (5L, 950),\n",
        " (6L, 736),\n",
        " (7L, 536),\n",
        " (8L, 506),\n",
        " (10L, 345),\n",
        " (9L, 323)]"
       ]
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "Counter(distribution_intersect).most_common(10)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 19,
       "text": [
        "[(1L, 21595),\n",
        " (2L, 4018),\n",
        " (3L, 1819),\n",
        " (4L, 1187),\n",
        " (5L, 950),\n",
        " (6L, 736),\n",
        " (7L, 536),\n",
        " (8L, 506),\n",
        " (10L, 345),\n",
        " (9L, 323)]"
       ]
      }
     ],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "foo = khmer.load_hashbits(\"BFH_NoIndex_L003_R1.R10_FOX2_FD11H.fastq.gz.kh\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import khmer"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /nas3/gpratt/projects/encode/fastq/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/nas/nas0/gpratt/projects/encode/fastq\n"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "rparser = khmer.ReadParser(\"BFH_NoIndex_L003_R1.R10_FOX2_FD11H.fastq.gz\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "rparser2 = khmer.ReadParser(\"BFH_NoIndex_L003_R1.R02_FOX2_FB11H.fastq.gz\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ht = khmer.new_hashbits(25, 5e7, 4)\n",
      "ht2 = khmer.new_hashbits(25, 5e7, 4)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 31
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ht.consume_fasta_with_reads_parser(rparser)\n",
      "ht2.consume_fasta_with_reads_parser(rparser2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 32,
       "text": [
        "(32418567, 551115639L)"
       ]
      }
     ],
     "prompt_number": 32
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ht.save(\"BFH_NoIndex_L003_R1.R10_FOX2_FD11H.fastq.gz.hb\")\n",
      "ht2.save(\"BFH_NoIndex_L003_R1.R02_FOX2_FB11H.fastq.gz.hb\")"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "(n_unique, n_overlap, list) = ht.count_overlap(\"BFH_NoIndex_L003_R1.R02_FOX2_FB11H.fastq.gz\", ht2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "... consume_fasta 100000 1700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 200000 3400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 300000 5100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 400000 6800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 500000 8500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 600000 10200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 700000 11900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 800000 13600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 900000 15300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1000000 17000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1100000 18700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1200000 20400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1300000 22100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1400000 23800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1500000 25500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1600000 27200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1700000 28900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1800000 30600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 1900000 32300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2000000 34000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2100000 35700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2200000 37400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2300000 39100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2400000 40800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2500000 42500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2600000 44200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2700000 45900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2800000 47600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 2900000 49300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3000000 51000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3100000 52700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3200000 54400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3300000 56100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3400000 57800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3500000 59500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3600000 61200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3700000 62900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3800000 64600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 3900000 66300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4000000 68000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4100000 69700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4200000 71400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4300000 73100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4400000 74800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4500000 76500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4600000 78200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4700000 79900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4800000 81600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 4900000 83300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5000000 85000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5100000 86700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5200000 88400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5300000 90100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5400000 91800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5500000 93500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5600000 95200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5700000 96900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5800000 98600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 5900000 100300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6000000 102000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6100000 103700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6200000 105400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6300000 107100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6400000 108800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6500000 110500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6600000 112200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6700000 113900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6800000 115600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 6900000 117300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7000000 119000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7100000 120700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7200000 122400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7300000 124100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7400000 125800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7500000 127500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7600000 129200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7700000 130900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7800000 132600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 7900000 134300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8000000 136000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8100000 137700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8200000 139400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8300000 141100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8400000 142800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8500000 144500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8600000 146200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8700000 147900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8800000 149600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 8900000 151300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9000000 153000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9100000 154700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9200000 156400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9300000 158100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9400000 159800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9500000 161500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9600000 163200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9700000 164900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9800000 166600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 9900000 168300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10000000 170000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10100000 171700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10200000 173400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10300000 175100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10400000 176800000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10500000 178500000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10600000 180200000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10700000 181900000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10800000 183600000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 10900000 185300000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 11000000 187000000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 11100000 188700000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 11200000 190400000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 11300000 192100000\n",
        "..."
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " consume_fasta 11400000 193800000\n",
        "..."
       ]
      },
      {
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       "stream": "stdout",
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        " 'add_stop_tag',\n",
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        " 'assign_partition_id',\n",
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        " 'consume_fasta_and_tag',\n",
        " 'consume_fasta_and_tag_with_reads_parser',\n",
        " 'consume_fasta_and_tag_with_stoptags',\n",
        " 'consume_fasta_and_traverse',\n",
        " 'consume_fasta_with_reads_parser',\n",
        " 'consume_partitioned_fasta',\n",
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        " 'count_kmers_on_radius',\n",
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        " 'save_subset_partitionmap',\n",
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        " 'set_partition_id',\n",
        " 'subset_count_partitions',\n",
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        " 'traverse_from_reads',\n",
        " 'traverse_from_tags',\n",
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 ]
}