bradely_2013_review.ipynb

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import glob\n",
      "\n",
      "import pandas as pd\n",
      "from IPython.core.display import HTML\n",
      "\n",
      "from gscripts.general import parsers"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "iclip_df = parsers.clipseq_metrics(\"/nas3/gpratt/projects/reviews/2013_bradley/analysis/bradely_clipseq_v1/\", iclip=True)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "iclip_df[\"Reads After Triming\"] = iclip_df['Processed reads'] - iclip_df['Too short reads']\n",
      "filtered_df = iclip_df[[\"Processed reads\",\n",
      "                        \"Reads After Triming\",\n",
      "                        \"Number of input reads\", \n",
      "                        \"Uniquely mapped reads number\",\n",
      "                        \"Uniquely mapped reads %\",\n",
      "                        \"Usable Reads\",\n",
      "                        #\"spot\",\n",
      "                        \"Num Peaks\"\n",
      "                            ]] "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "HTML(filtered_df.ix[[name for name in filtered_df.index if len(name.split(\".\")[1].split(\"_\")) > 1]].to_html(formatters={\"Processed reads\" : parsers.commas,\n",
      "                                     \"Reads After Triming\" : parsers.commas,\n",
      "                                     \"Number of input reads\" : parsers.commas,\n",
      "                                     \"Uniquely mapped reads number\" : parsers.commas,\n",
      "                                     \"Usable Reads\" : parsers.commas,\n",
      "                                     \"Num Peaks\": parsers.commas\n",
      "                                     }))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": [
        "<table border=\"1\" class=\"dataframe\">\n",
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>Processed reads</th>\n",
        "      <th>Reads After Triming</th>\n",
        "      <th>Number of input reads</th>\n",
        "      <th>Uniquely mapped reads number</th>\n",
        "      <th>Uniquely mapped reads %</th>\n",
        "      <th>Usable Reads</th>\n",
        "      <th>Num Peaks</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>B52.R01_B52-1_a</th>\n",
        "      <td> 58,163,022</td>\n",
        "      <td> 58,017,164</td>\n",
        "      <td>  57,815,416</td>\n",
        "      <td>  3,172,214</td>\n",
        "      <td>  5.49%</td>\n",
        "      <td>  400,712</td>\n",
        "      <td> 21</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>B52.R08_B52-2_a</th>\n",
        "      <td> 56,097,865</td>\n",
        "      <td> 55,966,192</td>\n",
        "      <td>  55,787,390</td>\n",
        "      <td>  1,943,919</td>\n",
        "      <td>  3.48%</td>\n",
        "      <td>   89,689</td>\n",
        "      <td> 50</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>D0KTJACXX_1.R02_SF2-2_c</th>\n",
        "      <td>  4,408,076</td>\n",
        "      <td>  4,394,384</td>\n",
        "      <td>   3,312,545</td>\n",
        "      <td>    425,633</td>\n",
        "      <td> 12.85%</td>\n",
        "      <td>   40,328</td>\n",
        "      <td>  1</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>D0KTJACXX_1.R07_SF2-1_c</th>\n",
        "      <td>  4,524,905</td>\n",
        "      <td>  4,511,658</td>\n",
        "      <td>   4,103,119</td>\n",
        "      <td>    219,073</td>\n",
        "      <td>  5.34%</td>\n",
        "      <td>   30,992</td>\n",
        "      <td>  1</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>D0KTJACXX_2.R02_SC35-2_c</th>\n",
        "      <td>123,737,936</td>\n",
        "      <td>123,492,293</td>\n",
        "      <td> 120,777,406</td>\n",
        "      <td> 12,231,550</td>\n",
        "      <td> 10.13%</td>\n",
        "      <td>   56,198</td>\n",
        "      <td> 41</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>D0KTJACXX_2.R08_B52-2_b</th>\n",
        "      <td>103,968,077</td>\n",
        "      <td>103,754,380</td>\n",
        "      <td> 103,235,347</td>\n",
        "      <td> 10,447,771</td>\n",
        "      <td> 10.12%</td>\n",
        "      <td>  211,273</td>\n",
        "      <td>266</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1.R09_Rbp1-1_c</th>\n",
        "      <td> 73,737,643</td>\n",
        "      <td> 73,394,309</td>\n",
        "      <td>  72,529,775</td>\n",
        "      <td>  1,104,489</td>\n",
        "      <td>  1.52%</td>\n",
        "      <td>  273,355</td>\n",
        "      <td> 52</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1.R13_Rbp1-2_c</th>\n",
        "      <td> 62,225,254</td>\n",
        "      <td> 61,867,085</td>\n",
        "      <td>  61,529,450</td>\n",
        "      <td>    533,136</td>\n",
        "      <td>  0.87%</td>\n",
        "      <td>  103,934</td>\n",
        "      <td> 18</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like.R11_Rbp1Like-1_c</th>\n",
        "      <td> 87,062,626</td>\n",
        "      <td> 86,789,082</td>\n",
        "      <td>  86,537,117</td>\n",
        "      <td>  1,625,567</td>\n",
        "      <td>  1.88%</td>\n",
        "      <td>  310,091</td>\n",
        "      <td> 70</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like.R12_Rbp1Like-2_c</th>\n",
        "      <td> 88,694,365</td>\n",
        "      <td> 88,418,682</td>\n",
        "      <td>  88,085,184</td>\n",
        "      <td>  3,553,214</td>\n",
        "      <td>  4.03%</td>\n",
        "      <td>  299,204</td>\n",
        "      <td> 89</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like_H.R11_Rbp1Like-1_a</th>\n",
        "      <td>  8,853,736</td>\n",
        "      <td>  8,819,395</td>\n",
        "      <td>   6,538,931</td>\n",
        "      <td>  3,219,033</td>\n",
        "      <td> 49.23%</td>\n",
        "      <td>  603,913</td>\n",
        "      <td>164</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like_H.R12_Rbp1Like-2_a</th>\n",
        "      <td>  7,518,617</td>\n",
        "      <td>  7,490,716</td>\n",
        "      <td>   5,119,367</td>\n",
        "      <td>  2,578,678</td>\n",
        "      <td> 50.37%</td>\n",
        "      <td>  451,020</td>\n",
        "      <td>108</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like_H2.R11_Rbp1Like-1_b</th>\n",
        "      <td> 12,163,130</td>\n",
        "      <td> 12,117,577</td>\n",
        "      <td>   9,029,725</td>\n",
        "      <td>  4,458,637</td>\n",
        "      <td> 49.38%</td>\n",
        "      <td>  682,258</td>\n",
        "      <td>194</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1Like_H2.R12_Rbp1Like-2_b</th>\n",
        "      <td> 10,201,939</td>\n",
        "      <td> 10,165,842</td>\n",
        "      <td>   7,008,667</td>\n",
        "      <td>  3,525,172</td>\n",
        "      <td> 50.30%</td>\n",
        "      <td>  503,885</td>\n",
        "      <td>121</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1_H.R09_Rpb1-1_a</th>\n",
        "      <td> 30,618,912</td>\n",
        "      <td> 30,423,416</td>\n",
        "      <td>  19,264,394</td>\n",
        "      <td>  7,503,652</td>\n",
        "      <td> 38.95%</td>\n",
        "      <td>  523,721</td>\n",
        "      <td>120</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1_H.R13_Rbp1-2_a</th>\n",
        "      <td> 19,491,728</td>\n",
        "      <td> 19,330,124</td>\n",
        "      <td>  13,788,148</td>\n",
        "      <td>  4,682,322</td>\n",
        "      <td> 33.96%</td>\n",
        "      <td>  319,369</td>\n",
        "      <td>141</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1_H2.R09_Rbp1-1_b</th>\n",
        "      <td> 96,879,963</td>\n",
        "      <td> 96,532,093</td>\n",
        "      <td>  62,531,076</td>\n",
        "      <td> 24,293,127</td>\n",
        "      <td> 38.85%</td>\n",
        "      <td>  558,827</td>\n",
        "      <td>142</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rbp1_H2.R13_Rbp2_b</th>\n",
        "      <td> 61,339,598</td>\n",
        "      <td> 61,052,392</td>\n",
        "      <td>  44,625,905</td>\n",
        "      <td> 14,931,935</td>\n",
        "      <td> 33.46%</td>\n",
        "      <td>  379,224</td>\n",
        "      <td>226</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rsf1.R03_Rsf1-1_b</th>\n",
        "      <td> 64,194,990</td>\n",
        "      <td> 64,149,643</td>\n",
        "      <td>  64,130,531</td>\n",
        "      <td>     51,664</td>\n",
        "      <td>  0.08%</td>\n",
        "      <td>   18,956</td>\n",
        "      <td>  9</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rsf1.R04_Rsf1-2_b</th>\n",
        "      <td> 49,966,456</td>\n",
        "      <td> 49,936,671</td>\n",
        "      <td>  49,922,283</td>\n",
        "      <td>     58,040</td>\n",
        "      <td>  0.12%</td>\n",
        "      <td>   16,301</td>\n",
        "      <td>  7</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rsf1_H.R03_Rsf1-1_a</th>\n",
        "      <td> 10,999,695</td>\n",
        "      <td> 10,952,121</td>\n",
        "      <td>  10,121,673</td>\n",
        "      <td>  2,705,478</td>\n",
        "      <td> 26.73%</td>\n",
        "      <td>        0</td>\n",
        "      <td>  0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>Rsf1_H.R04_Rsf1-2_a</th>\n",
        "      <td>  9,710,954</td>\n",
        "      <td>  9,671,124</td>\n",
        "      <td>   9,218,198</td>\n",
        "      <td>  1,524,127</td>\n",
        "      <td> 16.53%</td>\n",
        "      <td>   89,685</td>\n",
        "      <td>  6</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SC35.R02_SC35-2_a</th>\n",
        "      <td> 53,543,840</td>\n",
        "      <td> 53,484,596</td>\n",
        "      <td>  53,460,442</td>\n",
        "      <td>     95,934</td>\n",
        "      <td>  0.18%</td>\n",
        "      <td>   16,611</td>\n",
        "      <td>  8</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SC35.R07_SC35-1_b</th>\n",
        "      <td> 62,682,029</td>\n",
        "      <td> 62,636,956</td>\n",
        "      <td>  62,619,708</td>\n",
        "      <td>     60,574</td>\n",
        "      <td>  0.10%</td>\n",
        "      <td>   23,470</td>\n",
        "      <td> 12</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SC35_H.R02_SC35-2_b</th>\n",
        "      <td> 82,222,614</td>\n",
        "      <td> 82,032,113</td>\n",
        "      <td>  80,043,714</td>\n",
        "      <td>  8,856,853</td>\n",
        "      <td> 11.07%</td>\n",
        "      <td>   42,480</td>\n",
        "      <td> 19</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SC35_H.R07_SC35-1_b</th>\n",
        "      <td> 82,057,995</td>\n",
        "      <td> 81,819,215</td>\n",
        "      <td>  80,502,731</td>\n",
        "      <td> 10,034,887</td>\n",
        "      <td> 12.47%</td>\n",
        "      <td>  231,530</td>\n",
        "      <td>349</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SF2.R02_SF2-2_b</th>\n",
        "      <td>112,291,304</td>\n",
        "      <td>112,173,652</td>\n",
        "      <td> 112,078,755</td>\n",
        "      <td>    112,721</td>\n",
        "      <td>  0.10%</td>\n",
        "      <td>   25,882</td>\n",
        "      <td> 11</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SF2.R07_SF2-1_b</th>\n",
        "      <td> 64,365,753</td>\n",
        "      <td> 64,324,037</td>\n",
        "      <td>  64,276,525</td>\n",
        "      <td>     45,886</td>\n",
        "      <td>  0.07%</td>\n",
        "      <td>   19,263</td>\n",
        "      <td>  9</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SF2_H.R02_SF2-2_a</th>\n",
        "      <td> 45,784,336</td>\n",
        "      <td> 45,658,533</td>\n",
        "      <td>  34,770,738</td>\n",
        "      <td>  4,481,956</td>\n",
        "      <td> 12.89%</td>\n",
        "      <td>  120,124</td>\n",
        "      <td> 23</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SF2_H.R07_SF2-1_a</th>\n",
        "      <td> 43,670,732</td>\n",
        "      <td> 43,563,351</td>\n",
        "      <td>  39,765,492</td>\n",
        "      <td>  2,140,876</td>\n",
        "      <td>  5.38%</td>\n",
        "      <td>   98,208</td>\n",
        "      <td> 14</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRp54.R14_SRp54-1_b</th>\n",
        "      <td>114,940,027</td>\n",
        "      <td>114,657,182</td>\n",
        "      <td> 114,472,320</td>\n",
        "      <td>    265,368</td>\n",
        "      <td>  0.23%</td>\n",
        "      <td>   63,891</td>\n",
        "      <td> 13</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRp54.R15_SRp54-2_b</th>\n",
        "      <td>109,376,086</td>\n",
        "      <td>109,196,982</td>\n",
        "      <td> 109,092,119</td>\n",
        "      <td>    187,613</td>\n",
        "      <td>  0.17%</td>\n",
        "      <td>   83,474</td>\n",
        "      <td> 13</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRp54_H.R14_SRp54-1_a</th>\n",
        "      <td> 72,007,611</td>\n",
        "      <td> 71,377,675</td>\n",
        "      <td>  54,279,251</td>\n",
        "      <td> 20,804,971</td>\n",
        "      <td> 38.33%</td>\n",
        "      <td>  835,440</td>\n",
        "      <td>217</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>SRp54_H.R15_SRp54-2_a</th>\n",
        "      <td> 79,885,433</td>\n",
        "      <td> 79,356,305</td>\n",
        "      <td>  69,050,125</td>\n",
        "      <td> 18,118,493</td>\n",
        "      <td> 26.24%</td>\n",
        "      <td>1,511,716</td>\n",
        "      <td>374</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>XL6.R05_XL6-1_a</th>\n",
        "      <td>117,112,192</td>\n",
        "      <td>116,409,719</td>\n",
        "      <td> 115,555,014</td>\n",
        "      <td>  9,556,992</td>\n",
        "      <td>  8.27%</td>\n",
        "      <td>1,700,828</td>\n",
        "      <td>236</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>XL6.R06_XL6-2_a</th>\n",
        "      <td>105,902,381</td>\n",
        "      <td>105,538,671</td>\n",
        "      <td> 104,856,648</td>\n",
        "      <td>  8,868,582</td>\n",
        "      <td>  8.46%</td>\n",
        "      <td>2,199,327</td>\n",
        "      <td>409</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>"
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 25,
       "text": [
        "<IPython.core.display.HTML at 0x15889510>"
       ]
      }
     ],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "3000000000.0 / 135000000 "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 14,
       "text": [
        "22.22222222222222"
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}