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Include also panel name in mane report
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Chiara Rasi committed Oct 7, 2024
1 parent 1936018 commit da23b6f
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Showing 2 changed files with 9 additions and 1 deletion.
3 changes: 2 additions & 1 deletion src/chanjo2/meta/handle_report_contents.py
Original file line number Diff line number Diff line change
Expand Up @@ -258,13 +258,14 @@ def get_mane_overview_coverage_stats(query: ReportQuery, session: Session) -> Di
mane_stats = {
"levels": get_ordered_levels(threshold_levels=query.completeness_thresholds),
"extras": {
"hgnc_gene_ids": [hgnc_gene_ids]
"hgnc_gene_ids": hgnc_gene_ids
or query.hgnc_gene_ids
or query.hgnc_gene_symbols
or query.ensembl_gene_ids,
"interval_type": query.interval_type.value,
"completeness_thresholds": query.completeness_thresholds,
"samples": [_serialize_sample(sample) for sample in query.samples],
"panel_name": query.panel_name,
},
"interval_type": IntervalType.TRANSCRIPTS,
"samples_coverage_stats_by_interval": {},
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7 changes: 7 additions & 0 deletions src/chanjo2/templates/mane_overview.html
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,13 @@ <h2 class="accordion-header" id="flush-headingOne">

{% macro mane_stats_macro() %}
<h2>MANE Transcripts coverage report</h2>
{% if extras.panel_name %}
<p>
Final coverage metrics were calculated for genes from the clinical panels.
Note that <strong>estimations were made regarding coverage and completeness
on the level of {{ extras.interval_type }}</strong>.
</p>
{% endif %}
<br>
{% for interval_id, samples_stats in interval_coverage_stats.items() %}
<tr>
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