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 "metadata": {
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 },
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 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Steven and I are trying to ID target loci (lineage-specific and developmentally different loci). This is a check to make sure we can obtain the same result"
     ]
    },
    {
     "cell_type": "heading",
     "level": 4,
     "metadata": {},
     "source": [
      "Starting with the methratio files, I am going to filter for context and coverage. Then I will create files containing columns for loci ID and methylation information"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Output for methratio file\n",
      "methratio=\"/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_methratio_files/\"\n",
      "\n",
      "#Location of output files\n",
      "filtered=\"/Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_M1.txt> {filtered}methratio_out_M1_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_M1_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_M1.txt > {filtered}M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 38
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}SQL_M1.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci M1ratio\r\n",
        "C12768.103 0.167\r\n",
        "C12768.119 0.250\r\n",
        "C12768.145 0.000\r\n",
        "C12806.56 0.000\r\n",
        "C12806.76 0.200\r\n",
        "C12806.78 0.200\r\n",
        "C12806.105 0.250\r\n",
        "C12806.142 0.375\r\n",
        "C12924.19 0.000\r\n"
       ]
      }
     ],
     "prompt_number": 39
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T1D3.txt> {filtered}methratio_out_T1D3_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T1D3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 16
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T1D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_T1D3.txt > {filtered}T1D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 40
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}T1D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci T1D3ratio\r\n",
        "C12960.123 0.000\r\n",
        "C13208.83 1.000\r\n",
        "C13766.37 0.000\r\n",
        "C13766.42 0.000\r\n",
        "C13766.126 0.000\r\n",
        "C13766.145 0.000\r\n",
        "C13842.49 0.000\r\n",
        "C13874.46 0.000\r\n",
        "C13874.167 0.000\r\n"
       ]
      }
     ],
     "prompt_number": 41
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T1D5.txt> {filtered}methratio_out_T1D5_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T1D5_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T1D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T1D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 21
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_T1D5.txt > {filtered}T1D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 42
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}T1D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci T1D5ratio\r\n",
        "C12832.25 0.000\r\n",
        "C12960.67 0.000\r\n",
        "C12960.123 0.000\r\n",
        "C13040.69 0.000\r\n",
        "C13128.87 0.000\r\n",
        "C13208.148 0.333\r\n",
        "C13442.65 0.000\r\n",
        "C13442.79 0.000\r\n",
        "C13546.84 0.000\r\n"
       ]
      }
     ],
     "prompt_number": 43
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_M3.txt> {filtered}methratio_out_M3_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_M3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_M3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_M3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_M3.txt > {filtered}M3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 45
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}M3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci M3ratio\r\n",
        "C12806.142 0.000\r\n",
        "C12866.162 0.000\r\n",
        "C12960.123 0.000\r\n",
        "C12994.134 0.000\r\n",
        "C13046.76 0.000\r\n",
        "C13074.146 0.000\r\n",
        "C13080.102 0.000\r\n",
        "C13080.111 0.000\r\n",
        "C13080.130 0.000\r\n"
       ]
      }
     ],
     "prompt_number": 46
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T3D3.txt> {filtered}methratio_out_T3D3_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 27
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T3D3_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 28
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T3D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 29
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_T3D3.txt > {filtered}T3D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 49
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}T3D3.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci T3D3ratio\r\n",
        "C12768.103 0.000\r\n",
        "C12960.67 0.000\r\n",
        "C12960.123 0.000\r\n",
        "C12960.176 0.000\r\n",
        "C12960.186 0.000\r\n",
        "C13046.76 0.000\r\n",
        "C13208.148 0.333\r\n",
        "C13248.98 0.000\r\n",
        "C13390.79 0.000\r\n"
       ]
      }
     ],
     "prompt_number": 50
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!grep \"[A-Z][A-Z]CG[A-Z]\" <{methratio}methratio_out_T3D5.txt> {filtered}methratio_out_T3D5_CG.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 31
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_T3D5_CG.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 32
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!awk '{print ($1\".\"$2),$5}' </Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/methratio_out_CG3x_T3D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/SQL_T3D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 33
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!sed '/NA/d' {filtered}SQL_T3D5.txt > {filtered}T3D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 51
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!head {filtered}T3D5.txt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "loci T3D5ratio\r\n",
        "C12798.142 0.000\r\n",
        "C12798.145 0.000\r\n",
        "C12798.151 0.000\r\n",
        "C12960.67 0.000\r\n",
        "C12960.123 0.000\r\n",
        "C12994.63 0.000\r\n",
        "C12994.90 0.000\r\n",
        "C13128.87 0.000\r\n",
        "C13208.83 0.500\r\n"
       ]
      }
     ],
     "prompt_number": 52
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#NOTEBOOK NAME\n",
      "nb='ID_Target_Loci_Check'\n",
      "\n",
      "#NOTEBOOK LOCATION\n",
      "nbloc='/Users/claireolson/Dropbox/Lab\\ \\(1\\)/IPython_nbs/Claire/'\n",
      "\n",
      "\n",
      "\n",
      "#TIMESTAMP\n",
      "date=!date +%m%d_%H%M\n",
      "#LOCATION OF POST DIRECTORY\n",
      "post='/Volumes/web/Mollusk/iPython_Posts/'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 53
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd {post}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/Volumes/web/Mollusk/iPython_Posts\n"
       ]
      }
     ],
     "prompt_number": 54
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/ID_Target_Loci_Check.ipynb to html\r\n",
        "[NbConvertApp] Support files will be in ID_Target_Loci_Check[0716_1608]_files/\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Loaded template html_full.tpl\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[NbConvertApp] Writing 216231 bytes to ID_Target_Loci_Check[0716_1608].html\r\n"
       ]
      }
     ],
     "prompt_number": 55
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}