Added pangenomic class column to the locus tag table on the genome pa…

…ge and added phylogroup info to the info panel.
biosustain · Dec 20, 2024 · aee829e · aee829e
1 parent 1c5737c
commit aee829e
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Showing 4 changed files with 64 additions and 3 deletions.
diff --git a/gene_function/models.py b/gene_function/models.py
@@ -5,6 +5,58 @@
 class GeneInfo:
     objects = database.MongoDBObjects("pankb_gene_info")
 
+    def get_gene_info_and_pangenomic_class_pipeline(gene_match):
+        return [
+            {"$match": gene_match},
+            {
+                "$lookup": {
+                    "from": "pankb_gene_annotations",
+                    "let": {
+                        "q_gene": "$gene",
+                        "q_pangenome_analysis": "$pangenome_analysis",
+                    },
+                    "pipeline": [
+                        {
+                            "$match": {
+                                "$expr": {
+                                    "$and": [
+                                        {"$eq": ["$gene", "$$q_gene"]},
+                                        {
+                                            "$eq": [
+                                                "$pangenome_analysis",
+                                                "$$q_pangenome_analysis",
+                                            ]
+                                        },
+                                    ]
+                                }
+                            }
+                        }
+                    ],
+                    "as": "pangenomic_class",
+                }
+            },
+            {
+                "$set": {
+                    "pangenomic_class": {
+                        "$ifNull": [
+                            {"$arrayElemAt": ["$pangenomic_class.pangenomic_class", 0]},
+                            "-",
+                        ]
+                    }
+                }
+            },
+        ]
+
+    def get_gene_info_and_pangenomic_class(genome_match, projection=None):
+        pipeline = GeneInfo.get_gene_info_and_pangenomic_class_pipeline(genome_match)
+        if isinstance(projection, list):
+            projection = {p: 1 for p in projection}
+            if not "_id" in projection:
+                projection["_id"] = 0
+        if projection:
+            pipeline.append({"$project": projection})
+        return GeneInfo.objects.aggregate(pipeline)
+
 
 # Model for the Genome Info table content
 class GenomeInfo:

diff --git a/gene_function/views.py b/gene_function/views.py
@@ -214,13 +214,14 @@ def genome_info(request):
     genome_info_dict = _get_genome_and_isolation_info(filter_params)
 
     # Obtain the gene info: ----
-    gene_info = GeneInfo.objects.find(
+    gene_info = GeneInfo.get_gene_info_and_pangenomic_class(
         {"pangenome_analysis": species, "genome_id": genome_id},
         [
             "gene",
             "locus_tag",
             "pangenome_analysis",
             "genome_id",
+            "pangenomic_class",
             "original_locus_tag",
             "original_gene",
             "original_exact_match",
@@ -229,7 +230,7 @@ def genome_info(request):
             "end_position",
             "nucleotide_seq",
             "aminoacid_seq",
-        ],
+        ]
     )
     gene_info = list(gene_info)
 

diff --git a/templates/components/panel_locustags_table.html b/templates/components/panel_locustags_table.html
@@ -28,6 +28,7 @@
         <th class="text-center">Genome ID</th>
         {% else %}
         <th class="text-center">Gene</th>
+        <th class="text-center">Class</th>
         {% endif %}
         <th class="text-center">Protein</th>
         <th class="text-center">Start Position</th>
@@ -46,6 +47,7 @@
             <th class="text-center">Genome ID</th>
             {% else %}
             <th class="text-center">Gene</th>
+            <th class="text-center">Class</th>
             {% endif %}
             <th class="text-center">Protein</th>
             <th class="text-center">Start Position</th>
@@ -116,6 +118,9 @@
                         return '<a href="{% url 'gene_info' %}?species={{request.GET.species|safe}}&gene=' + encodeURIComponent(data) + '">' + data + '</a>';
                     },
                 },
+                {
+                    data: 'pangenomic_class',
+                },
                 {% endif %}
                 {
                     data: 'protein',

diff --git a/templates/gene_function/info_panel_genome_info.html b/templates/gene_function/info_panel_genome_info.html
@@ -11,9 +11,12 @@ <h6 class="card-subtitle mb-2 text-body-secondary display-6 pt-1"><a style="colo
 <dl class="row g-1 fs-3">
     <dt class="col-sm-12">Strain (<a href="https://www.ncbi.nlm.nih.gov/datasets/genome/{{dataGenome.genome_id|safe}}" target="_blank">NCBI</a>)</dt>
     <dd class="col-sm-12">{{ dataGenome.strain }}</dd>
-
+    <dt class="col-sm-6">Phylogroup</dt>
+    <dd class="col-sm-6">{{ dataGenome.phylo_group }}</dd>
+
     <dt class="col-sm-12">Isolation Source</dt>
     <dd class="col-sm-12">{{ dataGenome.isolation_source }}</dd>
+    <dt class="col-sm-12">Isolation Source Categories</dt>
     <dd class="col-sm-12">
       <ol class="breadcrumb" style="--bs-breadcrumb-divider: '>';">
         {% for category in dataGenome.iso_cat %}