Mercurial > repos > cpt > cpt_phageqc_annotations
diff cpt_phageqc_annotation/phageqc_report_464.html @ 0:c3140b08d703 draft default tip
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| author | cpt |
|---|---|
| date | Fri, 17 Jun 2022 13:00:50 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_phageqc_annotation/phageqc_report_464.html Fri Jun 17 13:00:50 2022 +0000 @@ -0,0 +1,419 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags --> + <meta name="description" content=""> + <meta name="author" content=""> + <title>[BICH464] Phage QC on {{record_name}} - {{score}}</title> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css"> + + <style type="text/css"> +/* + * Base structure + */ + +/* Move down content because we have a fixed navbar that is 50px tall */ +body { + padding-top: 50px; +} + +h3:before { + display: block; + content: " "; + margin-top: -50px; + height: 50px; + visibility: hidden; +} + +/* + * Global add-ons + */ + +.sub-header { + padding-bottom: 10px; + border-bottom: 1px solid #eee; +} + +/* + * Top navigation + * Hide default border to remove 1px line. + */ +.navbar-fixed-top { + border: 0; +} + +/* + * Sidebar + */ + +/* Hide for mobile, show later */ +.sidebar { + display: none; +} +@media (min-width: 768px) { + .sidebar { + position: fixed; + top: 51px; + bottom: 0; + left: 0; + z-index: 1000; + display: block; + padding: 20px; + overflow-x: hidden; + overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */ + background-color: #f5f5f5; + border-right: 1px solid #eee; + } +} + +/* Sidebar navigation */ +.nav-sidebar { + margin-right: -21px; /* 20px padding + 1px border */ + margin-bottom: 20px; + margin-left: -20px; +} +.nav-sidebar > li > a { + padding-right: 20px; + padding-left: 20px; +} +.nav-sidebar > .active > a, +.nav-sidebar > .active > a:hover, +.nav-sidebar > .active > a:focus { + color: #fff; + background-color: #428bca; +} + + +/* + * Main content + */ + +.main { + padding: 20px; +} +@media (min-width: 768px) { + .main { + padding-right: 40px; + padding-left: 40px; + } +} +.main .page-header { + margin-top: 0; +} + + +/* + * Placeholder dashboard ideas + */ + +.placeholders { + margin-bottom: 30px; + text-align: center; +} +.placeholders h4 { + margin-bottom: 0; +} +.placeholder { + margin-bottom: 20px; +} +.placeholder img { + display: inline-block; + border-radius: 50%; +} + + + + + + + +/* CUSTOM CSS */ +.spark { + position: relative; + margin:5px; +} +.spark span { + padding: 0px; + padding-left: 20px; + padding-right: 20px; + margin: 5px; + position: relative; +} +.spark .plus { + top: -10px; + background: #aaaaff; +} +.spark .minus { + top: 10px; + background: #ffaaaa; +} +.plus-focus { + top: -10px; + background: blue; +} +.minus-focus { + top: 10px; + background: red; +} + </style> + <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries --> + <!--[if lt IE 9]> + <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script> + <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> + <![endif]--> + </head> + <body> + + <nav class="navbar navbar-inverse navbar-fixed-top"> + <div class="container-fluid"> + <div class="navbar-header"> + <a class="navbar-brand" href="#">[BICH464] Phage QC on {{record_name}}</a> + </div> + </div> + </nav> + + <div class="container-fluid"> + <div class="row"> + <div class="col-sm-3 col-md-2 sidebar"> + <ul class="nav nav-sidebar"> + <li><a href="#main"><b>Overview</b></a></li> + <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li> + <li><a href="#missing_rbs"><small>Missing RBS</small></a></li> + <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li> + <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li> + <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li> + <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>--> + <li><a href="#gene_model"><b>Gene Model Issues</b></a></li> + </ul> + </div> + <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main"> + <div class="jumbotron"> + <div class="row"> + <div class="col-sm-7"> + <h1>Phage {{record_name}}</h1> + <!--<h2>Score: {{ '%d' % ((gene_model_score + coding_density + excessive_overlap_score + excessive_overlap_score + missing_rbs_score) / 5)}}</h2>--> + </div> + <!--<div class="col-sm-5"> + <table class="table table-striped"> + <thead> + <tr> + <th>Section</th> + <th>Score</th> + </tr> + </thead> + <tbody> + <tr><td>Missing RBS</td><td>{{ '%d' % missing_rbs_score }}%</td></tr> + <tr><td>Excessive Gaps</td><td>{{ '%d' % excessive_gap_score }}%</td></tr> + <tr><td>Excessive Overlap</td><td>{{ '%d' % excessive_overlap_score }}%</td></tr> + <tr><td>Coding Density Score</td><td>{{ '%d' % coding_density }}%</td></tr> + <tr><td>Coding Density Real</td><td>{{ '%0.2f' % (100 * coding_density_exact) }}%</td></tr> + <tr><td>Gene Model Issues</td><td>{{ '%d' % gene_model_score }}%</td></tr> + </tbody> + </table> + </div>--> + </div> + <div class="row"> + <h3>Genome Overview</h3> + <h4>Genes</h4> + <ul> + <li>Count: {{ genome_overview.genes.count }}</li> + <li>Bases: {{ genome_overview.genes.bases }}</li> + <li>Average Length: {{ genome_overview.genes.avg_len | round | int}}</li> + <li>Coding Density: {{ '%0.2f' % (100 * coding_density_exact) }}%</li> + <li>Composition + <ul> + <li>A {{ genome_overview.genes.comp.A }}</li> + <li>C {{ genome_overview.genes.comp.C }}</li> + <li>T {{ genome_overview.genes.comp.T }}</li> + <li>G {{ genome_overview.genes.comp.G }}</li> + </ul> + </li> + </ul> + <h4>Overall</h4> + <ul> + <li>%GC: {{ '%0.2f' % (100 * genome_overview.overall.gc) }}%</li> + <li>Composition + <ul> + <li>A {{ genome_overview.overall.comp.A }}</li> + <li>C {{ genome_overview.overall.comp.C }}</li> + <li>T {{ genome_overview.overall.comp.T }}</li> + <li>G {{ genome_overview.overall.comp.G }}</li> + </ul> + </li> + </ul> + </div> + </div> + + <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2> + <h3 id="missing_rbs">Genes Missing RBS <small>{{missing_rbs_good}} / {{missing_rbs_good + missing_rbs_bad}}</small></h3> + <p>The following genes have issues with their RBS.</p> + {% if not rbss_annotated %} + <p> + Since you have not annotated any possible RBSs, this does not count off from your overall score. + </p> + {% endif %} + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>ID</th> + <th>Location</th> + <th>Error</th> + <th>Upstream (-{{upstream_max}} .. -{{upstream_min}})</th> + </tr> + </thead> + <tbody> + {% for row in missing_rbs %} + {% if "None found" in row.__message %} + <tr> + <td>{{row | nice_id | decode}}</td> + <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td> + <td>None found</td> + <td><span style="font-family:monospace">{{row.__upstream }}</span></td> + </tr> + {% endif %} + {% endfor %} + </tbody> + </table> + </div> + + <h3 id="weird_starts">Start Codon Usage</h3> + <p>This section covers genes with unusual start codons</p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Start Codon</th> + <th>Count</th> + </tr> + </thead> + <tbody> + {% for codon_key in weird_starts_overall_sorted_keys %} + <tr><td>{{ codon_key }}</td><td>{{ weird_starts_overall[codon_key] }}</td></tr> + {% endfor %} + </tbody> + </table> + </div> + + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>ID</th> + <th>Location</th> + <th>Error</th> + </tr> + </thead> + <tbody> + {% for row in weird_starts %} + <tr> + <td>{{row | nice_id| decode}}</td> + <td>{{row.location.start}}..{{row.location.end}} [{{row.strand}}]</td> + <td>{{row.qualifiers.get('note', [])}}</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + + <h3 id="excessive_gaps">Intergenic Gaps</h3> + <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> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Region</th> + <th>Size</th> + <th>Bounding Gene Transcription Direction</th> + <th>Message</th> + </tr> + </thead> + <tbody> + {% for row in excessive_gap %} + <tr> + <td>{{row[0]}} .. {{row[1]}}</td> + <td>{{row[1] - row[0]}}</td> + <td>{{row[2] | nice_strand}} {{row[3] | nice_strand}}</td> + <td> + {% if row[4] == 0 %} + {% else %} + {{row[4]}} possible genes found in this region + {% endif %} + </td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + + <h3 id="excessive_overlap">Overlapping Genes</h3> + <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature A</th> + <th>Feature B</th> + <th>Shared Region</th> + <th>Overlap Length</th> + </tr> + </thead> + <tbody> + {% for row in excessive_overlap %} + <tr> + <td>{{row[0] | nice_id | decode}} ({{row[0].location}})</td> + <td>{{row[1] | nice_id | decode}} ({{row[1].location}})</td> + <td>{{row[2]}}..{{row[3]}}</td> + <td>{{row[3] - row[2]}}bp</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + <!--<h3 id="coding_density">Coding Density Issues <small>{{ coding_density }} / 100</small></h3> + <div class="table-responsive"> + <p> + You have a coding density score of {{ coding_density_real }} which scores + {{ coding_density }} / 100. Most genomes should be in the 90% to + 100% coding density range. Your exact coding density is {{ coding_density_exact }}. + </p> + </div>--> + + <h2 class="sub-header" id="gene_model">Gene Model Issues</h2> + <p>These issues are mostly derived from how Apollo handles the gene model. <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAMsAAAAUCAYAAAAjk8nJAAAABmJLR0QA/wD/AP+gvaeTAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH4AIRECEhlCV0dQAAAPBJREFUaN7t20EKgkAUxvFnlBASiBewNm7HldA+ukQH6AhtukBH6ABdIqJtIIS6dVNdoCtMm8CN1gtb6f+3GmQ28/DjzeDoWGutAPhqQAkAnSElQB0n6M9a7ZOwoKV43/015uuWnWW2q8a3Tf1zgDML0DNpepSyvLTfhh1OFBMd34rldzEmlCw7i+eNJYrmnFmAJkXxEBH5GBrCAihDQ1gAZWg44ANKdBaghjGhuO6IbRjwS0joLIAyJOqwrBbVeHulqOieOJ6K708aQ0JnAd6SZKma5/A/C2pfjKA/Fym1t44JCxrD0heEBfgzPkoCSi/B1kHb2fpwrwAAAABJRU5ErkJggg=="></p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>ID</th> + <th>Exon</th> + <th>CDS</th> + <th>Message</th> + </tr> + </thead> + <tbody> + {% for row in gene_model %} + <tr> + <td>{{row[0]}}</td> + <td>{{row[1].location}}</td> + <td>{{row[2].location}}</td> + <td>{{row[3]}}</td> + </tr> + {% endfor %} + </tbody> + </table> + </div> + + </div> + </div> + </div> + + + <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script> + </body> +</html> +