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[% # FOREACH row IN vep_data; '<pre>'; row; '</pre>'; END %]

[% # PROCESS dumper.tt dump = params %]
[% # PROCESS dumper.tt dump = results.samples.match %]
[% # PROCESS dumper.tt dump = results.exon_ref %]
[% # PROCESS dumper.tt dump = natural_sort([1,3,'d','a']) %]

<div class="container">
    <p>
        <a href="#results">vep results [[% results.vep_data.size || 0 %]]</a> ::
        <a href="#failures">sample match failures [[% results.samples.no_match.size || 0 %]]</a> ::
        <a href="#orphans">ophans [[% results.orphans.size || 0 %]]</a> ::
        <a href="/vep">new dataset</a>
    </p>
    
    <h5>
        [% total = results.row_count; duration = results.runtime; %]
        Processed [% total || 0 %] accepted rows in [% duration | format('%.2f') %]
        seconds ([% total / duration | format('%.1f') %]/sec)
    </h5>

    <h2>Sample results [[% results.samples.match.size %] samples]</h2>
    
    <table>
        <thead>
            <tr>
                <th>HMDS ref</th>
                <th>Exon</th>
                <th>Result</th>
                <th>Consequence</th>
                <th>Existing</th>
                <th>SIFT</th>
                <th>PolyPhen</th>
            </tr>
        </thead>
        [% FOREACH lab_number IN nsort_labno(results.samples.match.keys);
                # PROCESS dumper.tt dump = pair;
            location_data = results.samples.match.item(lab_number);
                # PROCESS dumper.tt dump = location_data;
            
            FOREACH pair IN location_data; # PROCESS dumper.tt dump = entry;
                location = pair.key; # PROCESS dumper.tt dump = location;
                result   = pair.value; # PROCESS dumper.tt dump = result;                
                vep_data = results.exon_ref.item(location); # PROCESS dumper.tt dump = vep;
            %]
            <tr>
                <td>[% result.hmds_ref %]</td>
                <td>[% vep_data.exon.replace('%%', ' ') %]</td>
                <td>[% result.result %]% of [% result.read %]</td>
                <td>[% vep_data.consequence %]</td>
                <td>[% vep_data.existing %]</td>
                <td>[% vep_data.sift %]</td>
                <td>[% vep_data.polyphen %]</td>
            </tr>                
        [% END; END %]
    </table>
    
    <h2><a name="failures">Sample match failures [[% results.samples.no_match.size %] samples]</a></h2>
    <table>
        <thead>
            <tr>
                <th>HMDS ref</th>
                <th>Exon</th>
                <th>Consequence</th>
                <th>Existing</th>
                <th>Other</th>
            </tr>
        </thead>
        [% FOREACH lab_number IN nsort_labno(results.samples.no_match.keys);
                # PROCESS dumper.tt dump = pair;
            location_data = results.samples.no_match.item(lab_number);
                # PROCESS dumper.tt dump = location_data;

            FOREACH pair IN location_data; # PROCESS dumper.tt dump = entry;
                location = pair.key; # PROCESS dumper.tt dump = location;
                result   = pair.value; # PROCESS dumper.tt dump = result;                
                vep_data = results.exon_ref.item(location); # PROCESS dumper.tt dump = vep;
            %]
            <tr>
                <td>[% result.hmds_ref %]</td>
                <td>[% vep_data.exon.replace('%%', ' ') %]</td>
                <td>[% vep_data.consequence %]</td>
                <td>[% vep_data.existing %]</td>
                <td>
                    [% '? orphan' IF ( NOT vep_data.consequence AND
                        NOT vep_data.existing ) %]
                </td>
            </tr>                
        [% END; END %]
    </table>

    <h2><a name="results">VEP results [[% results.vep_data.size %]]</a></h2>
    
    <table>
        <thead>
            <tr>
                <th></th>
                <th>ID</th>
                <th>Chr.</th>
                <th>Start</th>
                <th>End</th>
                <th>Allele</th>
                <th>Consequence</th>
                <th>AA</th>
                <th>Existing variation</th>
                [%# sift & poly order dependant on VEP::_prediction_and_score() %]
                [% IF params.sift %]<th>SIFT</th>[% END %]
                [% IF params.polyphen %]<th>PolyPhen</th>[% END %]
                <th>Extra</th>
            </tr>
        </thead>
        [% FOREACH row IN results.vep_data %]
            <tr>
                <td align="right">[% loop.count %]</td>
                [% FOREACH col IN row;
                    IF loop.first; # exon ID - prevent wrapping: %]
                    <td>[% col.replace('%%', ' ') %]</td>
                    [% ELSE %]<td>[% col | html %]</td>[% END %]
                [% END %]
            </tr>
        [% END %]
    </table>
    
    <h2><a name="orphans">VEP orphans [[% results.orphans.size %]]</a></h2>
    <table>
        <thead>
            <tr>
                <th></th>
                <th>ID</th>
                <th>Chr.</th>
                <th>Start</th>
                <th>End</th>
                <th>Allele</th>
            </tr>
        </thead>
        [% FOREACH row IN results.orphans %]
            <tr>
                <td align="right">[% loop.count %]</td>
                <td>[% row.exon.replace('%%', ' ') %]</td>
                <td>[% row.chromosome %]</td>
                <td>[% row.start_point %]</td>
                <td>[% row.end_point %]</td>
                <td>[% row.allele %]</td>
            </tr>
        [% END %]
    </table>
</div>