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1 <!DOCTYPE html>
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2 <html lang="en">
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3 <head>
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4 <meta charset="utf-8">
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5 <meta http-equiv="X-UA-Compatible" content="IE=edge">
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6 <meta name="viewport" content="width=device-width, initial-scale=1">
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7 <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
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8 <meta name="description" content="">
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9 <meta name="author" content="">
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10 <title>Phage QC on {{record_name}} - {{score}}</title>
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11 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
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12 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
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13
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14 <style type="text/css">
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15 /*
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16 * Base structure
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17 */
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18
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19 /* Move down content because we have a fixed navbar that is 50px tall */
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20 body {
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21 padding-top: 50px;
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22 }
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23
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24 h3:before {
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25 display: block;
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26 content: " ";
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27 margin-top: -50px;
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28 height: 50px;
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29 visibility: hidden;
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30 }
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31
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32 /*
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33 * Global add-ons
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34 */
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35
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36 .sub-header {
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37 padding-bottom: 10px;
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38 border-bottom: 1px solid #eee;
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39 }
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40
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41 /*
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42 * Top navigation
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43 * Hide default border to remove 1px line.
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44 */
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45 .navbar-fixed-top {
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46 border: 0;
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47 }
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48
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49 /*
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50 * Sidebar
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51 */
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52
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53 /* Hide for mobile, show later */
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54 .sidebar {
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55 display: none;
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56 }
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57 @media (min-width: 768px) {
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58 .sidebar {
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59 position: fixed;
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60 top: 51px;
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61 bottom: 0;
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62 left: 0;
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63 z-index: 1000;
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64 display: block;
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65 padding: 20px;
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66 overflow-x: hidden;
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67 overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
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68 background-color: #f5f5f5;
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69 border-right: 1px solid #eee;
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70 }
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71 }
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72
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73 /* Sidebar navigation */
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74 .nav-sidebar {
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75 margin-right: -21px; /* 20px padding + 1px border */
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76 margin-bottom: 20px;
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77 margin-left: -20px;
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78 }
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79 .nav-sidebar > li > a {
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80 padding-right: 20px;
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81 padding-left: 20px;
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82 }
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83 .nav-sidebar > .active > a,
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84 .nav-sidebar > .active > a:hover,
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85 .nav-sidebar > .active > a:focus {
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86 color: #fff;
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87 background-color: #428bca;
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88 }
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89
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90
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91 /*
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92 * Main content
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93 */
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94
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95 .main {
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96 padding: 20px;
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97 }
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98 @media (min-width: 768px) {
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99 .main {
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100 padding-right: 40px;
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101 padding-left: 40px;
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102 }
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103 }
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104 .main .page-header {
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105 margin-top: 0;
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106 }
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107
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108
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109 /*
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110 * Placeholder dashboard ideas
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111 */
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112
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113 .placeholders {
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114 margin-bottom: 30px;
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115 text-align: center;
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116 }
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117 .placeholders h4 {
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118 margin-bottom: 0;
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119 }
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120 .placeholder {
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121 margin-bottom: 20px;
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122 }
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123 .placeholder img {
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124 display: inline-block;
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125 border-radius: 50%;
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126 }
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127
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128 td.moron {
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129 font-size: 150%;
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130 padding: 0px;
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131 color: gray;
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132 }
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133 .strand_emph {
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134 text-decoration: underline;
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135 color: black;
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136 }
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137
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138 </style>
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139 <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
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140 <!--[if lt IE 9]>
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141 <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
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142 <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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143 <![endif]-->
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144 </head>
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145 <body>
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146
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147 <nav class="navbar navbar-inverse navbar-fixed-top">
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148 <div class="container-fluid">
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149 <div class="navbar-header">
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150 <a class="navbar-brand" href="#">Phage QC on {{record_name}}</a>
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151 </div>
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152 </div>
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153 </nav>
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154
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155 <div class="container-fluid">
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156 <div class="row">
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157 <div class="col-sm-3 col-md-2 sidebar">
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158 <ul class="nav nav-sidebar">
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159 <li><a href="#main"><b>Overview</b></a></li>
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160 <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li>
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161 <li><a href="#missing_rbs"><small>Missing RBS</small></a></li>
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162 <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li>
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163 <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li>
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164 <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li>
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165 <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>-->
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166 <li><a href="#antisense"><b>Antisense Genes</b></a></li>
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167 <li><a href="#morons"><small>Possible Morons</small></a></li>
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168 <li><a href="#annotations"><b>Annotation Issues</b></a></li>
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169 <li><a href="#missing_product"><small>Missing Product Tags</small></a></li>
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170 </ul>
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171 </div>
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172 <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main">
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173 <div class="jumbotron">
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174 <div class="row">
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175 <div class="col-sm-7">
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176 <h1>Phage {{record_name}}</h1>
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177 <!--<h2>Score: {{score}}/100</h2>-->
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178 </div>
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179 <!--<div class="col-sm-5">
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180 <table class="table table-striped">
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181 <thead>
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182 <tr>
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183 <th>Section</th>
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184 <th>Score</th>
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185 </tr>
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186 </thead>
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187 <tbody>
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188 <tr><td>Missing RBS</td><td>{{ '%d' % missing_rbs_score }}%</td></tr>
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189 <tr><td>Excessive Gaps</td><td>{{ '%d' % excessive_gap_score }}%</td></tr>
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190 <tr><td>Excessive Overlap</td><td>{{ '%d' % excessive_overlap_score }}%</td></tr>
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191 <tr><td>Coding Density Score</td><td>{{ '%d' % coding_density }}%</td></tr>
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192 <tr><td>Possible Morons</td><td>{{ '%d' % (100 * morons_good / (morons_good + morons_bad))}}%</td></tr>
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193 <tr><td>Missing Product Tags</td><td>{{ '%d' % (100 * missing_tags_good / (missing_tags_good + missing_tags_bad))}}%</td></tr>
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194 </tbody>
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195 </table>
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196 </div>-->
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197 </div>
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198 </div>
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199
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200 <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2>
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201 <h3 id="missing_rbs">Genes missing RBS <small>{{missing_rbs_good}} / {{missing_rbs_good + missing_rbs_bad}}</small></h3>
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202 <p>The following genes have issues with their RBS.</p>
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203 {% if not rbss_annotated %}
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204 <p>
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205 Since you have not annotated any possible RBSs, this does not count off from your overall score.
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206 </p>
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207 {% endif %}
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208 <div class="table-responsive">
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209 <table class="table table-striped">
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210 <thead>
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211 <tr>
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212 <th>Feature Type</th>
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213 <th>ID</th>
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214 <th>Location</th>
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215 <th>Error</th>
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216 <th>Upstream (-{{upstream_max}} .. -{{upstream_min}})</th>
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217 </tr>
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218 </thead>
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219 <tbody>
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220 {% for row in missing_rbs %}
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221 <tr>
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222 <td>{{row.type}}</td>
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223 <td>{{row.id}}</td>
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224 <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td>
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225 <td>{{row.__message}}</td>
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226 <td><span style="font-family:monospace">{{row.__upstream}}</span></td>
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227 </tr>
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228 {% endfor %}
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229 </tbody>
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230 </table>
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231 </div>
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232
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233 <h3 id="weird_starts">Start Codon Usage</h3>
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234 <p>This section covers genes with unusual start codons</p>
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235 <div class="table-responsive">
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236 <table class="table table-striped">
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237 <thead>
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238 <tr>
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239 <th>Start Codon</th>
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240 <th>Count</th>
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241 </tr>
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242 </thead>
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243 <tbody>
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244 {% for codon_key in weird_starts_overall_sorted_keys %}
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245 <tr><td>{{ codon_key }}</td><td>{{ weird_starts_overall[codon_key] }}</td></tr>
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246 {% endfor %}
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247 </tbody>
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248 </table>
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249 </div>
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250
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251 <div class="table-responsive">
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252 <table class="table table-striped">
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253 <thead>
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254 <tr>
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255 <th>Feature Type</th>
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256 <th>ID</th>
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257 <th>Location</th>
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258 <th>Error</th>
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259 </tr>
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260 </thead>
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261 <tbody>
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262 {% for row in weird_starts %}
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263 <tr>
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264 <td>{{row.type}}</td>
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265 <td>{{row.id}}</td>
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266 <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td>
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267 <td>{{row.__error}}</td>
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268 </tr>
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269 {% endfor %}
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270 </tbody>
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271 </table>
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272 </div>
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273
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274 <h3 id="excessive_gaps">Intergenic Gaps</h3>
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275 <p>Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.</p>
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276 <div class="table-responsive">
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277 <table class="table table-striped">
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278 <thead>
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279 <tr>
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280 <th>Region</th>
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281 <th>Size</th>
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282 <th>Bounding Gene Transcription Direction</th>
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283 <th>Message</th>
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284 </tr>
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285 </thead>
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286 <tbody>
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287 {% for row in excessive_gap %}
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288 <tr>
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289 <td>{{row[0]}} .. {{row[1]}}</td>
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290 <td>{{row[1] - row[0]}}</td>
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291 <td>{{row[2] | nice_strand}} {{row[3] | nice_strand}}</td>
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292 <td>
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293 {% if row[4] == 0 %}
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294 {% else %}
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295 {{row[4]}} ORFs found in this region
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296 {% endif %}
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297 </td>
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298 </tr>
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299 {% endfor %}
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300 </tbody>
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301 </table>
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302 </div>
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303
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304 <h3 id="excessive_overlap">Overlapping Genes </h3>
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305 <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p>
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306 <div class="table-responsive">
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307 <table class="table table-striped">
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308 <thead>
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309 <tr>
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310 <th>Feature A</th>
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311 <th>Feature B</th>
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312 <th>Shared Region</th>
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313 <th>Overlap Length</th>
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314 </tr>
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315 </thead>
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316 <tbody>
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317 {% for row in excessive_overlap %}
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318 <tr>
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319 <td>{{row[0].id}} ({{row[0].location}})</td>
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320 <td>{{row[1].id}} ({{row[1].location}})</td>
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321 <td>{{row[2]}}..{{row[3]}}</td>
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322 <td>{{row[3] - row[2]}} bp</td>
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323 </tr>
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324 {% endfor %}
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325 </tbody>
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326 </table>
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327 </div>
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328 <!--<h3 id="coding_density">Coding Density Issues <small>{{ coding_density }} / 100</small></h3>
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329 <div class="table-responsive">
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330 <p>
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331 You have a coding density of {{ coding_density_real }} which scores
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332 {{ coding_density }} / 100. Most genomes should be in the 90% to
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333 100% coding density range
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334 </p>
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335 </div>-->
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336
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337 <h2 class="sub-header" id="antisense">Antisense Genes</h2>
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338 <h3 id="morons">Possible Morons <small>{{morons_good}} / {{morons_good + morons_bad}} (Doesn't count towards score)</small></h3>
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339 <div class="table-responsive">
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340 <table class="table table-striped">
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341 <thead>
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342 <tr>
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343 <th>Feature</th>
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344 <th>RBS</th>
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345 <th>Surrounding Features</th>
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346 </tr>
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347 </thead>
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348 <tbody>
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349 {% for row in morons %}
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350 <tr>
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351 <td>{{row[0].id}}</td>
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352 <td>{{row[3]}}</td>
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353 <td class="moron">
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354 {% for x in row[1] %}
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355 {{ x | nice_strand }}
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356 {% endfor %}
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357 <span class="strand_emph">{{ row[0].strand | nice_strand }}</span>
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358 {% for x in row[2] %}
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359 {{ x | nice_strand }}
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360 {% endfor %}
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361 </div>
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362 </td>
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363 </tr>
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364 {% endfor %}
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365 </tbody>
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366 </table>
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367 </div>
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368
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369
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370 <h2 class="sub-header" id="annotations">Annotation Issues</h2>
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371 <h3 id="missing_product">Missing Product Tags <small>{{missing_tags_good}} / {{missing_tags_good + missing_tags_bad}}</small></h3>
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372 <div class="table-responsive">
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373 <table class="table table-striped">
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374 <thead>
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375 <tr>
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376 <th>Feature</th>
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377 <th>Qualifiers</th>
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378 </tr>
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379 </thead>
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380 <tbody>
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381 {% for row in missing_tags %}
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382 <tr>
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383 <td>{{row.id}}</td>
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384 <td>
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385 {% for key in row.qualifiers %}
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386 {{ key }}
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387 <ul>
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388 {% for value in row.qualifiers[key] %}
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389 <li>{{value}}</li>
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390 {% endfor %}
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391 </ul>
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392 {% endfor %}
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393 </td>
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394 </tr>
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395 {% endfor %}
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396 </tbody>
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397 </table>
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398 </div>
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399
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400
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401
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402
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403
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404 </div>
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405 </div>
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406 </div>
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407
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408
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409 <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
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410 </body>
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411 </html>
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412
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