bugfix d2_algo

deconvolution/d2graph/d2_algorithms.py

 import networkx as nx
 
-from deconvolution.d2graph.d2_path import Unitig
+# from deconvolution.d2graph.d2_path import Unitig
 
 
 """ Remove unnecessary transitions
@@ -84,87 +84,87 @@ def filter_singeltons(graph):
     return graph
 
 
-""" Compute the unambiguous paths in a d2g. The d2g must not contain singletons.
-    The unitigs are sorted by increasing penalty first and decreasing size second.
-    @param d2g a d2g graph
-    @return a list of unitigs
-"""
-def compute_unitigs(d2g):
-    unitigs = []
-    used_nodes = {int(node): False for node in d2g.nodes()}
-
-    for node_id in d2g.nodes():
-        node_idx = int(node_id)
-        node = d2g.node_by_idx[node_idx]
-
-        # If already tested
-        if used_nodes[node.idx]:
-            continue
-        used_nodes[node.idx] = True
-
-        if d2g.degree(str(node.idx)) > 2:
-            # Not a unitig
-            continue
-
-        # Create new unitigs
-        unitig = compute_unitig_from(d2g, node)
-        unitigs.append(unitig)
-        for node in unitig:
-            used_nodes[node.idx] = True
-
-    # Sort the unitigs
-    unitigs.sort(key=lambda x: (x.normalized_penalty(), -len(x)))
-
-    return unitigs
-
-
-""" Compute a unitig starting from the node regarding the graph.
-    The unitig will be extended on both sides
-    @param d2g The d2g to look for unitig
-    @param node The start node of the unitig
-    @return The constructed unitig
-"""
-def compute_unitig_from(d2g, node):
-    unitig = Unitig(d2g)
-    unitig.add_path([node])
-    if d2g.degree(str(node.idx)) == 2:
-        left, right = d2g.neighbors(str(node.idx))
-    else:
-        left = next(d2g.neighbors(str(node.idx)))
-        right = None
-
-    # Extends first side
-    prev_node = node
-    current_node = d2g.node_by_idx[int(left)]
-    unitig = extend_unitig(unitig, d2g, prev_node, current_node)
-    unitig.revert()
-
-    # Extends second side
-    prev_node = node
-    current_node = d2g.node_by_idx[int(right)] if right is not None else None
-    unitig = extend_unitig(unitig, d2g, prev_node, current_node)
-
-    return unitig
-
-
-""" Directional extension of the unitig. Uses the previous and current nodes to detect the extension direction.
-    @param unitig The unitig to extend. Will be modified during the execution.
-    @param d2g The d2g to follow for extension
-    @param prev_node Node already added in the unitig
-    @param current_node Node to add into the unitig and used to select the next node to add. If not set, stop the extension.
-    @return Return the modified unitig. 
-"""
-def extend_unitig(unitig, d2g, prev_node, current_node):
-    if current_node is None:
-        return unitig
-
-    # Add the node
-    unitig.add_right(current_node)
-
-    # Look for the next node
-    next_candidates = list(d2g.neighbors(str(current_node.idx)))
-    next_candidates.remove(str(prev_node.idx))
-    # Select next node
-    next_node = d2g.node_by_idx[int(next_candidates[0])] if len(next_candidates) == 1 else None
-    # Continue extension
-    return extend_unitig(unitig, d2g, current_node, next_node)
+# """ Compute the unambiguous paths in a d2g. The d2g must not contain singletons.
+#     The unitigs are sorted by increasing penalty first and decreasing size second.
+#     @param d2g a d2g graph
+#     @return a list of unitigs
+# """
+# def compute_unitigs(d2g):
+#     unitigs = []
+#     used_nodes = {int(node): False for node in d2g.nodes()}
+#
+#     for node_id in d2g.nodes():
+#         node_idx = int(node_id)
+#         node = d2g.node_by_idx[node_idx]
+#
+#         # If already tested
+#         if used_nodes[node.idx]:
+#             continue
+#         used_nodes[node.idx] = True
+#
+#         if d2g.degree(str(node.idx)) > 2:
+#             # Not a unitig
+#             continue
+#
+#         # Create new unitigs
+#         unitig = compute_unitig_from(d2g, node)
+#         unitigs.append(unitig)
+#         for node in unitig:
+#             used_nodes[node.idx] = True
+#
+#     # Sort the unitigs
+#     unitigs.sort(key=lambda x: (x.normalized_penalty(), -len(x)))
+#
+#     return unitigs
+#
+#
+# """ Compute a unitig starting from the node regarding the graph.
+#     The unitig will be extended on both sides
+#     @param d2g The d2g to look for unitig
+#     @param node The start node of the unitig
+#     @return The constructed unitig
+# """
+# def compute_unitig_from(d2g, node):
+#     unitig = Unitig(d2g)
+#     unitig.add_path([node])
+#     if d2g.degree(str(node.idx)) == 2:
+#         left, right = d2g.neighbors(str(node.idx))
+#     else:
+#         left = next(d2g.neighbors(str(node.idx)))
+#         right = None
+#
+#     # Extends first side
+#     prev_node = node
+#     current_node = d2g.node_by_idx[int(left)]
+#     unitig = extend_unitig(unitig, d2g, prev_node, current_node)
+#     unitig.revert()
+#
+#     # Extends second side
+#     prev_node = node
+#     current_node = d2g.node_by_idx[int(right)] if right is not None else None
+#     unitig = extend_unitig(unitig, d2g, prev_node, current_node)
+#
+#     return unitig
+#
+#
+# """ Directional extension of the unitig. Uses the previous and current nodes to detect the extension direction.
+#     @param unitig The unitig to extend. Will be modified during the execution.
+#     @param d2g The d2g to follow for extension
+#     @param prev_node Node already added in the unitig
+#     @param current_node Node to add into the unitig and used to select the next node to add. If not set, stop the extension.
+#     @return Return the modified unitig.
+# """
+# def extend_unitig(unitig, d2g, prev_node, current_node):
+#     if current_node is None:
+#         return unitig
+#
+#     # Add the node
+#     unitig.add_right(current_node)
+#
+#     # Look for the next node
+#     next_candidates = list(d2g.neighbors(str(current_node.idx)))
+#     next_candidates.remove(str(prev_node.idx))
+#     # Select next node
+#     next_node = d2g.node_by_idx[int(next_candidates[0])] if len(next_candidates) == 1 else None
+#     # Continue extension
+#     return extend_unitig(unitig, d2g, current_node, next_node)