rearrangeing code to prepare new graphs !

proost · Nov 30, 2017 · 29dc9d9 · 29dc9d9
1 parent 4c88161
commit 29dc9d9
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Showing 4 changed files with 86 additions and 29 deletions.
diff --git a/conekt/controllers/ecc.py b/conekt/controllers/ecc.py
@@ -82,6 +82,26 @@ def ecc_graph_pair_json(ecc_id):
     """
     network, family = SequenceSequenceECCAssociation.get_ecc_pair_network(ecc_id)
 
+    network_cytoscape = CytoscapeHelper.parse_network(network)
+    network_cytoscape = CytoscapeHelper.add_descriptions_nodes(network_cytoscape)
+    network_cytoscape = CytoscapeHelper.add_family_data_nodes(network_cytoscape, family)
+    network_cytoscape = CytoscapeHelper.add_lc_data_nodes(network_cytoscape)
+    network_cytoscape = CytoscapeHelper.add_species_data_nodes(network_cytoscape)
+    network_cytoscape = CytoscapeHelper.connect_homologs(network_cytoscape)
+
+    return json.dumps(network_cytoscape)
+
+
+@ecc.route('/multi_json/')
+def ecc_graph_multi_json():
+    """
+    Returns a JSON object compatible with cytoscape.js that contains the ECC graph for a specific pair of sequences
+
+    :param ecc_id: internal ID of the sequence to sequence ECC relationship
+    :return: JSON object compatible with cytoscape.js
+    """
+    network, family = SequenceSequenceECCAssociation.get_ecc_multi_network(2, [230458, 35796, 162930])
+
     network_cytoscape = CytoscapeHelper.parse_network(network)
     network_cytoscape = CytoscapeHelper.add_descriptions_nodes(network_cytoscape)
     network_cytoscape = CytoscapeHelper.add_family_data_nodes(network_cytoscape, family)

diff --git a/conekt/helpers/cytoscape.py b/conekt/helpers/cytoscape.py
@@ -251,6 +251,28 @@ def add_depth_data_nodes(network):
 
         return colored_network
 
+    @staticmethod
+    def connect_homologs(network):
+        connected_network = deepcopy(network)
+        """
+        Add edges between homologous genes from different targets, family_id needs to be specified !
+        """
+
+        for i in range(len(connected_network['nodes']) - 1):
+            for j in range(i + 1, len(connected_network['nodes'])):
+                if connected_network['nodes'][i]['data']['family_id'] == connected_network['nodes'][j]['data']['family_id'] and connected_network['nodes'][i]['data']['family_id'] is not None:
+                    connected_network['edges'].append({
+                        'data': {'source': connected_network['nodes'][i]['data']['id'],
+                                 'target': connected_network['nodes'][j]['data']['id'],
+                                 'color': "#33D",
+                                 'homology_color': "#33D",
+                                 'edge_type': 'homology',
+                                 'ecc_pair_color': "#33D",
+                                 'homology': True}
+                    })
+
+        return connected_network
+
     @staticmethod
     def add_connection_data_nodes(network):
         """

diff --git a/conekt/models/relationships/sequence_sequence_ecc.py b/conekt/models/relationships/sequence_sequence_ecc.py
@@ -201,32 +201,47 @@ def get_ecc_pair_network(ecc_id):
                           "edge_type": "expression",
                           'ecc_pair_color': "#3D3"})
 
-        """
-        Add gene families to sequences
-        """
-        seq_fams = SequenceFamilyAssociation.query.filter(and_(SequenceFamilyAssociation.sequence_id.in_(sequences),
-                                                               SequenceFamilyAssociation.family.has(method_id=association.gene_family_method_id)
-                                                               )).all()
-
-        seq_to_fam = {sf.sequence_id: sf.gene_family_id for sf in seq_fams}
+        return {"nodes": nodes, "edges": edges}, association.gene_family_method_id
 
-        for i, node in enumerate(nodes):
-            nodes[i]['family_id'] = seq_to_fam[node['gene_id']] if node['gene_id'] in seq_to_fam.keys() else None
-
-        """
-        Add edges between homologous genes from different targets
-        """
-
-        for i in range(len(nodes) - 1):
-            for j in range(i + 1, len(nodes)):
-                if nodes[i]['family_id'] == nodes[j]['family_id'] and nodes[i]['family_id'] is not None:
-                    edges.append(
-                        {'source': nodes[i]['id'],
-                         'target': nodes[j]['id'],
-                         'homology_color': "#33D",
-                         'edge_type': 'homology',
-                         'ecc_pair_color': "#33D",
-                         'homology': True}
-                    )
-
-        return {"nodes": nodes, "edges": edges}, association.gene_family_method_id
+    @staticmethod
+    def get_ecc_multi_network(gf_method_id, sequence_ids):
+        associations = SequenceSequenceECCAssociation.query.\
+            filter(SequenceSequenceECCAssociation.gene_family_method_id == gf_method_id).\
+            filter(and_(SequenceSequenceECCAssociation.query_id.in_(sequence_ids),
+                        SequenceSequenceECCAssociation.target_id.in_(sequence_ids))).\
+            all()
+
+        nodes = []
+        edges = []
+        node_sequence_ids = []
+
+        for a in associations:
+            if a.query_id not in node_sequence_ids:
+                node_sequence_ids.append(a.query_id)
+                nodes.append({"id": a.query_sequence.name,
+                              "name": a.query_sequence.name,
+                              "species_id": a.query_sequence.species_id,
+                              "species_name": a.query_sequence.species.name,
+                              "gene_id": a.query_id,
+                              "gene_name": a.query_sequence.name,
+                              "network_method_id": a.query_network_method_id,
+                              "node_type": "query"})
+
+            if a.target_id not in node_sequence_ids:
+                node_sequence_ids.append(a.target_id)
+                nodes.append({"id": a.target_sequence.name,
+                              "name": a.target_sequence.name,
+                              "species_id": a.target_sequence.species_id,
+                              "species_name": a.target_sequence.species.name,
+                              "gene_id": a.target_id,
+                              "gene_name": a.target_sequence.name,
+                              "network_method_id": a.target_network_method_id,
+                              "node_type": "query"})
+
+            edges.append({"source": a.query_sequence.name,
+                          "target": a.target_sequence.name,
+                          "ecc_score": a.ecc,
+                          'ecc_pair_color': "#D33",
+                          "edge_type": "ecc"})
+
+        return {"nodes": nodes, "edges": edges}, gf_method_id
diff --git a/conekt/templates/expression_graph.html b/conekt/templates/expression_graph.html
@@ -111,7 +111,7 @@ <h1>ECC pair</h1>
                                     {% if sequence %}
                                     <li><a href="#" class="cy-edge-width" attr="ecc_width">ECC</a></li>
                                     {% endif %}
-                                    {% if not sequence %}
+                                    {% if not sequence and not ecc_pair %}
                                     <li><hr /></li>
                                     <li class="dropdown-header"><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='hrr') }}" data-target="#helpModal">HRR</abbr> Filter</li>
                                     <li><p><strong>Cutoff:</strong> <span id="cy-edge-score-value" class="text-muted">{{cutoff}}</span></p></li>