Merge pull request #379 from Clinical-Genomics/add_refseq_txs

Add refseq txs
Clinical-Genomics · Oct 28, 2024 · 78cbe89 · 78cbe89
2 parents 476c2ef + c81e28d
commit 78cbe89
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Showing 4 changed files with 32 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,6 @@
 ## [unreleased]
+### Added
+- Refseq transcripts names on coverage overview page
 ### Fixed
 - Addressed the `Starlette Denial of service (DoS) via multipart/form-data` by updating starlette library. among others
 

diff --git a/src/chanjo2/meta/handle_d4.py b/src/chanjo2/meta/handle_d4.py
@@ -58,6 +58,7 @@ def get_report_sample_interval_coverage(
     genes_covered_under_custom_threshold = set()
 
     for interval_nr, interval in enumerate(sql_intervals):
+
         if interval.ensembl_id in interval_ids:
             continue
         for threshold in completeness_thresholds:
@@ -86,6 +87,15 @@ def get_report_sample_interval_coverage(
                         interval_hgnc_symbol,
                         interval_hgnc_id,
                         interval.ensembl_id,
+                        (
+                            {
+                                "mane_select": interval.refseq_mane_select,
+                                "mane_plus_clinical": interval.refseq_mane_plus_clinical,
+                                "mrna": interval.refseq_mrna,
+                            }
+                            if isinstance(interval, SQLTranscript)
+                            else {}
+                        ),
                         sample_name,
                         round(interval_coverage_at_threshold * 100, 2),
                     )

diff --git a/src/chanjo2/meta/handle_report_contents.py b/src/chanjo2/meta/handle_report_contents.py
@@ -133,7 +133,11 @@ def get_report_data(
             db=session,
             interval_type=INTERVAL_TYPE_SQL_TYPE[query.interval_type],
             genes=genes,
-            transcript_tags=[TranscriptTag.REFSEQ_MRNA],
+            transcript_tags=[
+                TranscriptTag.REFSEQ_MANE_PLUS_CLINICAL,
+                TranscriptTag.REFSEQ_MANE_SELECT,
+                TranscriptTag.REFSEQ_MRNA,
+            ],
         )
 
     for sample in query.samples:

diff --git a/src/chanjo2/templates/overview.html b/src/chanjo2/templates/overview.html
@@ -49,11 +49,22 @@
 							<td>
 								<a href="#" onclick="getGeneStatsPage({{row[1]}});">
 									{{row[0]}}
-								</a>
+								</a> <!-- link to gene -->
 							</td>
-							<td>{{ row[2] }}</td>
-							<td>{{ row[3] }}</td>
-							<td class="text-right">{{ row[4] }}</td>
+							<td>
+								{{ row[2] }} <!-- Ensembl ID -->
+								{% if row[3].mane_select %}
+									<span class="badge bg-dark float-end ">MANE Select: {{row[3].mane_select}}</span>
+								{% endif %}
+								{% if row[3].mane_plus_clinical %}
+									<span class="badge bg-dark float-end">MANE Plus Clinical: {{row[3].mane_plus_clinical}}</span>
+								{% endif %}
+								{% if row[3].mrna %}
+									<span class="badge bg-secondary float-end">{{row[3].mrna}}</span>
+								{% endif %}
+							</td>
+							<td>{{ row[4] }}</td> <!-- sample name -->
+							<td class="text-right">{{ row[5] }}</td> <!-- coverage stats -->
 						</tr>
 					{% else %}
 						<tr>