Mercurial > repos > cpt > cpt_phageqc_annotations

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    <title>[BICH464] Phage QC on {{record_name}} - {{score}}</title>
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    <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>

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