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Feature/panel summary, solves #40 #42

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merged 5 commits into from
Jun 29, 2021
Merged

Feature/panel summary, solves #40 #42

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ae7ce1d
Add panel summary to normal gene panels
rernst Jun 8, 2021
f99559a
Update based on feedback
rernst Jun 8, 2021
c78bc50
Update QC text
rernst Jun 9, 2021
d417cf6
Update QC text
rernst Jun 9, 2021
0ca3711
Merge branch 'develop' into feature/panel_summary
rernst Jun 10, 2021
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6 changes: 6 additions & 0 deletions ExonCov/templates/sample.html
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
<thead>
<tr>
<th>Gene Panel</th>
<th>Summary</th>
<th>Size (bp)</th>
{% for type in measurement_types %}
<th>{{ measurement_types[type] }}</th>
Expand All @@ -60,6 +61,11 @@
{% for panel in panels %}
<tr>
<td><a href="{{ url_for('sample_panel', sample_id=sample.id, panel_id=panel) }}">{{ panels[panel]['name_version'] }}</a></td>
{% if panels[panel]['measurement_percentage15'] < panels[panel]['coverage_requirement_15'] %}
<td class="danger">Dekking {{ panels[panel]['name_version'] }} >15X = {{ panels[panel]['measurement_percentage15']|float|round(2) }}% ; QC failed.</td>
{% else %}
<td>Dekking {{ panels[panel]['name_version'] }} >15X = {{ panels[panel]['measurement_percentage15']|float|round(2) }}%.</td>
{% endif %}
<td>{{ panels[panel]['len'] }}</td>
{% for type in measurement_types %}
{{ render_panel_measurement_td(panels[panel][type], type, panels[panel]) }}
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21 changes: 20 additions & 1 deletion ExonCov/templates/sample_panel.html
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Expand Up @@ -12,7 +12,26 @@
<dt>Type</dt><dd>{{ sample.type }}</dd>
<dt>Sequencing runs</dt><dd><ul class="list-inline">{% for run in sample.sequencing_runs %}<li>{{ run }}</li>{% endfor %}</ul></dd>
<dt>Panel</dt><dd>{{ panel.name_version }} </dd>
<dt>Minimal % 15x</dt><dd>{{ panel.coverage_requirement_15 }}</dd>
<dt>Minimal % 15x</dt><dd><p>{{ panel.coverage_requirement_15 }}</p></dd>
<dt>Summary</dt><dd>
{% if panel_summary['measurement_percentage15'] < panel.coverage_requirement_15 %}
<p>Dekking {{ panel.name_version }} >15X = {{ panel_summary['measurement_percentage15']|float|round(2) }}% ; <code>QC failed</code>.</p>
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{% else %}
<p>Dekking {{ panel.name_version }} >15X = {{ panel_summary['measurement_percentage15']|float|round(2) }}%.</p>
{% endif %}
{% if panel.core_genes %}
{% if panel_summary['core_genes'] %}
Core genen met 15x dekking < 100%: {{panel_summary['core_genes']}}.<br>
{% else %}
Core genen met 15x dekking < 100%: geen.<br>
{% endif %}
{% endif %}
{% if panel_summary['genes_15'] %}
Genen met 15x dekking < 95%: {{panel_summary['genes_15']}}.<br>
{% else %}
Genen met 15x dekking < 95%: geen.<br>
{% endif %}
</dd>
</dl>
</div>

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18 changes: 17 additions & 1 deletion ExonCov/views.py
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Expand Up @@ -142,15 +142,31 @@ def sample_panel(sample_id, panel_id):
.filter_by(sample_id=sample.id)
.options(joinedload(Transcript.exons, innerjoin=True))
.options(joinedload(Transcript.gene))
.order_by(TranscriptMeasurement.measurement_percentage15.asc())
.all()
)

# Setup panel summary
panel_summary = {
'measurement_percentage15': weighted_average(
[tm[1].measurement_percentage15 for tm in transcript_measurements],
[tm[1].len for tm in transcript_measurements]
),
'core_genes': ', '.join(
['{}({}) = {:.2f}%'.format(tm[0].gene, tm[0], tm[1].measurement_percentage15) for tm in transcript_measurements if tm[0].gene in panel.core_genes and tm[1].measurement_percentage15 < 100]
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),
'genes_15': ', '.join(
['{}({}) = {:.2f}%'.format(tm[0].gene, tm[0], tm[1].measurement_percentage15) for tm in transcript_measurements if tm[0].gene not in panel.core_genes and tm[1].measurement_percentage15 < 95]
)
}

return render_template(
'sample_panel.html',
sample=sample,
panel=panel,
transcript_measurements=transcript_measurements,
measurement_types=measurement_types
measurement_types=measurement_types,
panel_summary=panel_summary
)


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