Merge branch 'master' of gitlab.pasteur.fr:ydufresne/10x-deconvolve

deconvolution/evaluate.py

@@ -167,17 +167,13 @@ def print_path_summary(frequencies, neighborhood, light_print=False, file_pointe
 
 # ------------- D2 Graph -------------
 
-def parse_dg_name(name):
-    name = name.replace("]", "").replace(' [', '[')
-    header, h1, h2 = name.split('[')
+def parse_dg_name(gr, name):
+    udg = nx.get_node_attributes(gr, 'udg')[name]
+    udg = udg.replace("]", "").replace(' [', '[')
+    central, h1, h2 = udg.split('[')
     
-    # Parse header
-    header = header.split(" ")
-    idx = central = score = -1
-    if len(header) == 3:
-        idx, central, score = header
-    else:
-        central, score = header
+    idx = name
+    score = nx.get_node_attributes(gr, 'score')[name]
 
     # Parse hands
     h1 = h1.split(', ')
@@ -267,7 +263,7 @@ def compute_next_nodes(d2_component):
 
     for node in d2_component.nodes():
         # Parse the current node name
-        head, h1, h2 = parse_dg_name(node)
+        head, h1, h2 = parse_dg_name(d2_component,node)
         next_nodes[node] = {}
         neighbors = list(d2_component.neighbors(node))
 
@@ -276,7 +272,7 @@ def compute_next_nodes(d2_component):
         for mol_idx in molecule_idxs:
             nexts = []
             for neighbor in neighbors:
-                nei_head, _, _ = parse_dg_name(neighbor)
+                nei_head, _, _ = parse_dg_name(d2_component,neighbor)
                 nei_mols = mols_from_node(nei_head[1])
                 nei_mols = [x for x in nei_mols if x > mol_idx]
                 
@@ -401,7 +397,7 @@ def verify_graph_edges(d2_component):
     udg_molecules_dict=dict()
     for node in d2_component.nodes():
         # Parse the current node name
-        head, c1, c2 = parse_dg_name(node)
+        head, c1, c2 = parse_dg_name(d2_component,node)
 
         # Construct the molecule(s) that this udg really 'reflects'
         # i.e. the udg has a central node and two cliques
@@ -440,10 +436,10 @@ def verify_graph_edges(d2_component):
     # Then: annotate edges as to whether they're real (their udg_molecule(s) are nearby) or fake
     for n1, n2 , data in d2_component.edges(data=True):
         # Parse the current node name
-        head, c1, c2 = parse_dg_name(n1)
+        head, c1, c2 = parse_dg_name(d2_component,n1)
         node_udg_molecules = udg_molecules_dict[head[0]]
         
-        n_head, n_c1, n_c2 = parse_dg_name(n2)
+        n_head, n_c1, n_c2 = parse_dg_name(d2_component,n2)
         neighbor_udg_molecules = udg_molecules_dict[n_head[0]]
        
         if nearby_udg_molecules(node_udg_molecules, neighbor_udg_molecules):
@@ -456,7 +452,7 @@ def verify_graph_edges(d2_component):
     # also, annotate nodes by their putative molecule found
     for n, data in d2_component.nodes(data=True):
         # Parse the current node name
-        head, c1, c2 = parse_dg_name(n)
+        head, c1, c2 = parse_dg_name(d2_component,n)
         node_udg_molecules = udg_molecules_dict[head[0]]
         data['udg_molecule']= '_'.join(list(map(str,node_udg_molecules)))
         
@@ -468,7 +464,7 @@ def verify_graph_edges(d2_component):
         nodes_to_remove = []
         for n, data in d2_component.nodes(data=True):
             # Parse the current node name
-            head, c1, c2 = parse_dg_name(n)
+            head, c1, c2 = parse_dg_name(d2_component,n)
             if "_" in data['udg_molecule'] or data['udg_molecule'] == '':
                 if "_" in data['udg_molecule']:
                     m1, m2 = list(map(int,data['udg_molecule'].split("_")))