Displaying disease gene icon also for SVs (#620).

Related-Issue: #620
Closes: #620
Projected-Results-Impact: none

HISTORY.rst

@@ -45,6 +45,7 @@ End-User Summary
 - Adding section presets for SV filtration (#616).
 - Adjusting SV filtration presets (#616).
 - Fix bug with thousand genomes frequencies in SV filtration (#619).
+- Displaying disease gene icon also for SVs (#620).
 
 Full Change List
 ================
@@ -85,6 +86,7 @@ Full Change List
 - Adding section presets for SV filtration (#616).
 - Adjusting SV filtration presets (#616).
 - Fix bug with thousand genomes frequencies in SV filtration (#619).
+- Displaying disease gene icon also for SVs (#620).
 
 ------
 v1.2.0

svs/queries.py

@@ -41,6 +41,7 @@
     ExtendQueryPartsBase,
     ExtendQueryPartsGenotypeDefaultBase,
     ExtendQueryPartsCaseJoinAndFilter as _ExtendQueryPartsCaseJoinAndFilter,
+    ExtendQueryPartsDiseaseGeneJoin as _ExtendQueryPartsDiseaseGeneJoin,
 )
 
 #: Logger to use in this module.
@@ -682,6 +683,11 @@ class EnsemblRegulatoryFeatureTypes(enum.Enum):
     TF_BINDING_SITE = "TF_binding_site"
 
 
+class ExtendQueryPartsDiseaseGeneJoin(_ExtendQueryPartsDiseaseGeneJoin):
+
+    gene_id_model = StructuralVariantGeneAnnotation
+
+
 class ExtendQueryPartsEnsemblRegulatoryJoinAndFilter(ExtendQueryPartsBase):
     """Extend ``QueryParts`` with information for ENSEMBL regulatory region overlap."""
 
@@ -951,6 +957,7 @@ def extend_selectable(self, query_parts):
     ExtendQueryPartsVistaEnhancerJoinAndFilter,
     ExtendQueryPartsRegMapJoinAndFilter,
     ExtendQueryPartsHgncJoin,
+    ExtendQueryPartsDiseaseGeneJoin,
 ]
 
 

svs/templates/svs/filter_result/row_sv.html

@@ -48,12 +48,15 @@
         <span class="text-muted">&empty; genes</span>
       {% else %}
         <div class="btn-group" role="group">
-          <button type="button" class="btn btn-outline-secondary sodar-list-btn">
+          <button type="button" class="btn btn-outline-secondary sodar-list-btn" {% if entry.disease_gene %}title="disease gene"{% endif %}>
             {% if not entry.symbol %}
               {{ entry.gene_id }}
             {% else %}
               {{ entry.symbol }}
             {% endif %}
+            {% if entry.disease_gene %}
+            <i class="iconify text-danger" data-icon="fa-regular:lightbulb"></i>
+            {% endif %}
           </button>
           <button
             class="btn btn-primary sodar-list-btn"

svs/views.py

@@ -92,7 +92,6 @@ def form_valid(self, form):
         query = SingleCaseFilterQuery(self.get_case_object(), get_engine())
         args = dict(form.cleaned_data)
         # TODO: variant types
-        print("XXX\n\n", args, "\n\nXXX")
         with contextlib.closing(query.run(args)) as results:
             context_data = self._fetch_context_data(form, results)
             context_data["elapsed_seconds"] = timezone.now() - before

variants/queries.py

@@ -1318,6 +1318,10 @@ def extend_selectable(self, query_parts):
 
 
 class ExtendQueryPartsDiseaseGeneJoin(ExtendQueryPartsBase):
+
+    # Model with the gene ID
+    gene_id_model = SmallVariant
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         if self.kwargs["database_select"] == "refseq":
@@ -1329,7 +1333,8 @@ def __init__(self, *args, **kwargs):
             select([column("id")])
             .select_from(GeneIdInHpo.sa)
             .where(
-                getattr(SmallVariant.sa, "%s_gene_id" % self.kwargs["database_select"]) == gene_id
+                getattr(self.gene_id_model.sa, "%s_gene_id" % self.kwargs["database_select"])
+                == gene_id
             )
             .lateral("disease_gene_subquery")
         )

variants/templates/variants/second_hit.html

@@ -2,7 +2,7 @@
 {% load variants_tags %}
 {% load humanize %}
 
-<table class="table table-sm table-striped table-hover" style="font-size: 11px;">
+<table class="table table-sm table-striped table-hover" style="font-size: 11px; table-layout: fixed;">
   <thead>
     <tr>
       <th scope="col"></th>
@@ -41,22 +41,22 @@
       <tr>
         <td class="text-right">{{ forloop.counter }}</td>
         <td>{{ small_var.chromosome }}:{{ small_var.start|intcomma }}</td>
-        <td>{{ small_var.reference }}</td>
-        <td>{{ small_var.alternative }}</td>
+        <td style="max-width: 50px;"><div class="sodar-overflow-container">{{ small_var.reference }}</div></td>
+        <td style="max-width: 50px;"><div class="sodar-overflow-container">{{ small_var.alternative }}</div></td>
         <td class="text-right">{{ small_var.gnomad_exomes_frequency }}</td>
         <td class="text-right">{{ small_var.gnomad_exomes_homozygous|intcomma }}</td>
         <td class="text-right">{{ small_var.gnomad_genomes_frequency }}</td>
         <td class="text-right">{{ small_var.gnomad_genomes_homozygous|intcomma }}</td>
         <td class="text-right">{{ small_var.inhouse_carriers|intcomma }}</td>
         <td class="text-right">{{ small_var.inhouse_hom_alt|intcomma }}</td>
         {% if small_var.hgvs_p == "p.=" %}
-          <td>{{ small_var.hgvs_c }}</td>
+          <td><div class="sodar-overflow-container">{{ small_var.hgvs_c }}</div></td>
         {% elif small_var.hgvs_c == "p.?" %}
-          <td>{{ small_var.hgvs_c }} / p.?</td>
+          <td><div class="sodar-overflow-container">{{ small_var.hgvs_c }} / p.?</div></td>
         {% else %}
-          <td>{{ small_var.hgvs_p }}</td>
+          <td><div class="sodar-overflow-container">{{ small_var.hgvs_p }}</div></td>
         {% endif %}
-        <td>{{ small_var.effect|join:";" }}</td>
+        <td><div class="sodar-overflow-container">{{ small_var.effect|join:";" }}</div></td>
         {% for name in samples %}
           {% with genotype=small_var.genotype|keyvalue:name %}
             <td class="text-center" data-order="{{ genotype|keyvalue:"gt" }}">