Added rewiring testing

References #27

src/pybel_tools/selection/rewiring.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+
+"""
+
+This module has functions that help produce random permutations over networks.
+
+Random permutations are useful in statistical testing over aggregate statistics.
+
+"""
+
+import random
+
+from ..utils import is_edge_consistent
+
+
+def all_edges_consistent(graph):
+    """Returns if all edges are consistent in a graph. Wraps :func:`pybel_tools.utils.is_edge_consistent`
+
+    :param graph: A BEL graph
+    :type graph: pybel.BELGraph
+    :return: Are all edges consistent
+    :rtype: bool
+    """
+    return all(is_edge_consistent(graph, u, v) for u, v in graph.edges_iter())
+
+
+def rewire_targets(graph, p):
+    """Rewires a graph's edges' target nodes
+
+
+    - For BEL graphs, assumes edge consistency (all edges between two given nodes are have the same relation)
+    - Doesn't make self-edges
+
+    :param graph: A BEL graph
+    :type graph: pybel.BELGraph
+    :param p: The probability of rewiring
+    :return: A rewired BEL graph
+    """
+
+    if not all_edges_consistent(graph):
+        raise ValueError('{} is not consistent'.format(graph))
+
+    bg = graph.copy()
+    nodes = bg.nodes()
+
+    for u, v in bg.edges():
+        if random.random() < p:
+            continue
+
+        w = random.choice(nodes)
+
+        while w == u or bg.has_edge(u, w):
+            w = random.choice(nodes)
+
+        bg.add_edge(w, v)
+        bg.remove_edge(u, v)
+
+    return bg

src/pybel_tools/utils.py

@@ -12,7 +12,7 @@
 from pandas import DataFrame
 
 from pybel.constants import ANNOTATIONS, CITATION_TYPE, CITATION_NAME, CITATION_REFERENCE, CITATION_DATE, \
-    CITATION_AUTHORS, CITATION_COMMENTS
+    CITATION_AUTHORS, CITATION_COMMENTS, RELATION
 
 
 def graph_edge_data_iter(graph):
@@ -183,3 +183,41 @@ def citation_to_tuple(citation):
         citation.get(CITATION_AUTHORS),
         citation.get(CITATION_COMMENTS)
     ])
+
+
+def is_edge_consistent(graph, u, v):
+    """Checks if all edges between two nodes have the same relation
+
+    :param graph: A BEL Graph
+    :type graph: pybel.BELGraph
+    :param u: The source BEL node
+    :type u: tuple
+    :param v: The target BEL node
+    :type v: tuple
+    :return: If all edges from the source to target node have the same relation
+    :rtype: bool
+    """
+    if not graph.has_edge(u, v):
+        raise ValueError('{} does not contain an edge ({}, {})'.format(graph, u, v))
+
+    return 0 == len(set(d[RELATION] for d in graph.edge[u][v].values()))
+
+
+def safe_add_edge(graph, u, v, k, d):
+    """Adds an edge while preserving negative keys, and paying no respect to positive ones
+
+    :param graph: A BEL Graph
+    :type graph: pybel.BELGraph
+    :param u: The source BEL node
+    :type u: tuple
+    :param v: The target BEL node
+    :type v: tuple
+    :param k: The edge key. If less than zero, corresponds to an unqualified edge, else is disregarded
+    :type k: int
+    :param d: The edge data dictionary
+    :type d: dict
+    """
+    if k < 0:
+        graph.add_edge(u, v, key=k, attr_dict=d)
+    else:
+        graph.add_edge(u, v, attr_dict=d)