remove execuption variability

.gitignore

 data/
+real_data/
 art/
 **/__pycache__/
 .pytest_cache/
 .idea/
 .snakemake/
+snake_tests/
+**/*.tmp

deconvolution/d2_graph.py

@@ -56,6 +56,7 @@ class D2Graph(nx.Graph):
 
 
     def construct_from_barcodes(self, index_size=3, verbose=True, debug=False):
+        import debug_disct as dd
         # Compute all the d-graphs
         if verbose:
             print("Compute the unit d-graphs")
@@ -228,19 +229,6 @@ class D2Graph(nx.Graph):
             print()
             print("\tDmer removal")
 
-        # # Remove dominated in global list
-        # for r_idx, r_dg in enumerate(to_remove):
-        #
-        #     self.all_d_graphs.remove(r_dg)
-        #     self.d_graphs_per_node[r_dg.center].remove(r_dg)
-        #
-        #     Remove from index
-        #     for idx, dmer in enumerate(itertools.combinations(r_dg.to_sorted_list(), tuple_size)):
-        #         if dmer in self.index[dmer]:
-        #             self.index[dmer].remove(r_dg)
-        #             if len(self.index[dmer]) == 0:
-        #                 del self.index[dmer]
-
         removable_dmers = set()
         for r_idx, r_dg in enumerate(to_remove):
             if verbose:

deconvolution/d_graph.py

 import networkx as nx
-import math
 from functools import total_ordering
 
 
@@ -19,6 +18,8 @@ class Dgraph(object):
         self.ordered_list = None
         self.sorted_list = None
 
+        self.marked = False
+
 
     """ Static method to load a dgraph from a text
         @param text the saved d-graph
@@ -56,11 +57,13 @@ class Dgraph(object):
         self.halves[0] = h1
         for node in h1:
             self.node_set.add(node)
+            self.nodes.append(node)
         self.halves[1] = h2
         for node in h2:
             self.node_set.add(node)
+            self.nodes.append(node)
 
-        self.nodes = sorted([self.center] + self.halves[0] + self.halves[1])
+        # self.nodes = sorted([self.center] + self.halves[0] + self.halves[1])
         self.connexity[0] = {key: 0 for key in self.halves[0]}
         self.connexity[1] = {key: 0 for key in self.halves[1]}
         self.edges = []
@@ -174,7 +177,7 @@ class Dgraph(object):
         if other is None:
             return False
 
-        if self.idx == other.idx:
+        if self.idx != -1 and self.idx == other.idx:
             return True
 
         if self.node_set != other.node_set:
@@ -218,6 +221,11 @@ class Dgraph(object):
         representation += "[" + ", ".join([f"{node} {self.connexity[1][node]}" for node in self.halves[1]]) + "]"
         return representation
 
+    def _to_str_nodes(self):
+        str_nodes = [str(x) for x in self.nodes]
+        str_nodes.sort()
+        return str(str_nodes)
+
 
 """ From a barcode graph, compute all the possible max d-graphs by node.
     @param graph A barcode graph
@@ -243,15 +251,11 @@ def compute_all_max_d_graphs(graph, debug=False):
                 d_graph = Dgraph(node)
                 d_graph.put_halves(clq1, clq2, neighbors_graph)
 
-                if d_graph.get_link_divergence() > d_graph.get_optimal_score() / 2:
-                    continue
-
-                node_d_graphs.add(d_graph)
+                if d_graph.get_link_divergence() <= d_graph.get_optimal_score() / 2:
+                    node_d_graphs.add(d_graph)
 
-        # Cut the the distribution queue
 
         d_graphs[node] = sorted(node_d_graphs)
-        # print(node_d_graphs)
 
     return d_graphs
 
@@ -278,7 +282,6 @@ def add_new_dg_regarding_domination(dg, undominated_dgs_list):
     size = len(undominated_dgs_list)
     for dg2 in to_remove:
         undominated_dgs_list.remove(dg2)
-    #print(size, len(to_remove), len(undominated_dgs_list))
 
     # Add the new dg
     if not dominated:
@@ -296,9 +299,7 @@ def filter_dominated(d_graphs, overall=False, in_place=True):
     for dgs in d_graphs.values():
         all_d_graphs.extend(dgs)
 
-    # print(len(all_d_graphs))
     all_d_graphs = list_domination_filter(all_d_graphs)
-    # print(len(all_d_graphs))
 
     return d_graphs
 
@@ -316,8 +317,8 @@ def local_domination_filter(d_graphs, in_place=True):
 
     # Filter node by node
     for node, d_graph_list in d_graphs.items():
-        # Add the non filtered d-graph to the output
-        filtered[node] = brutal_list_domination_filter(d_graph_list)
+        lst = str(sorted([str(x) for x in d_graph_list]))
+        filtered[node] = brutal_list_domination_filter(d_graph_list, node_name=str(node))
 
     return filtered
 
@@ -337,13 +338,14 @@ def list_domination_filter(d_graphs):
 
     return set(filtered)
 
-def brutal_list_domination_filter(d_graphs):
+def brutal_list_domination_filter(d_graphs, node_name=""):
     undominated = set(d_graphs)
+    to_remove = set()
 
     for dg1 in d_graphs:
         for dg2 in d_graphs:
             if dg1.is_dominated(dg2):
-                undominated.remove(dg1)
+                to_remove.add(dg1)
                 break
 
-    return undominated
+    return undominated - to_remove