diff --git a/deconvolution/d2graph/d2_graph.py b/deconvolution/d2graph/d2_graph.py
index 45d92b6f9f5b76122506ad2f3d22b7759fca43c7..6eb32bb5f19122b0e182ca25f19852031e263aaa 100644
--- a/deconvolution/d2graph/d2_graph.py
+++ b/deconvolution/d2graph/d2_graph.py
@@ -12,26 +12,18 @@ from deconvolution.dgraph.LouvainDGFactory import LouvainDGFactory
class D2Graph(nx.Graph):
"""D2Graph (read it (d-graph)²)"""
- def __init__(self, barcode_graph, debug=False, debug_path='.'):
+ def __init__(self, debug=False, debug_path='.'):
super(D2Graph, self).__init__()
self.all_d_graphs = []
self.d_graphs_per_node = {}
self.node_by_idx = {}
- self.barcode_graph = barcode_graph
+ self.barcode_graph = None
self.index = None
self.variables_per_lcp = {}
- # Number the edges from original graph
self.barcode_edge_idxs = {}
self.nb_uniq_edge = 0
- for idx, edge in enumerate(self.barcode_graph.edges()):
- if edge == (edge[1], edge[0]):
- self.nb_uniq_edge += 1
- if edge in self.barcode_edge_idxs:
- print("Edge already present")
- self.barcode_edge_idxs[edge] = idx
- self.barcode_edge_idxs[(edge[1], edge[0])] = idx
self.debug = debug
self.debug_path = debug_path
@@ -64,7 +56,19 @@ class D2Graph(nx.Graph):
return self.subgraph(list(self.nodes()))
- def construct_from_barcodes(self, neighbor_threshold=0.25, min_size_clique=4, verbose=False, clique_mode=None, threads=1):
+ def construct_from_barcodes(self, barcode_graph, neighbor_threshold=0.25, min_size_clique=4, verbose=False, clique_mode=None, threads=1):
+ self.barcode_graph = barcode_graph
+
+ # Number the edges from original graph
+ for idx, edge in enumerate(self.barcode_graph.edges()):
+ if edge == (edge[1], edge[0]):
+ self.nb_uniq_edge += 1
+ if edge in self.barcode_edge_idxs:
+ print("Edge already present")
+ self.barcode_edge_idxs[edge] = idx
+ self.barcode_edge_idxs[(edge[1], edge[0])] = idx
+ self.barcode_graph[edge[0]][edge[1]]["uniq_idx"] = idx
+
# Compute all the d-graphs
if verbose:
print("Computing the unit d-graphs..")
@@ -181,7 +185,7 @@ class D2Graph(nx.Graph):
nodes[dg] = dg.idx
self.add_node(nodes[dg])
# Add covering barcode edges
- barcode_edges = " ".join([str(self.barcode_edge_idxs[x]) for x in dg.edges])
+ barcode_edges = " ".join([str(x) for x in dg.edges])
self.nodes[nodes[dg]]["barcode_edges"] = barcode_edges
self.nodes[nodes[dg]]["score"] = f"{dg.score}/{dg.get_optimal_score()}"
self.nodes[nodes[dg]]["udg"] = str(dg)
diff --git a/deconvolution/dgraph/d_graph.py b/deconvolution/dgraph/d_graph.py
index 496b9474f9a7924a85e6be3a0629140515563d6f..1d49a3ccdf403b453e39a1bb0947d7fc824bd14c 100644
--- a/deconvolution/dgraph/d_graph.py
+++ b/deconvolution/dgraph/d_graph.py
@@ -11,60 +11,57 @@ class Dgraph(object):
self.center = center
self.score = 0
self.halves = [[], []]
- self.connexity = [[], []]
+ self.connexity = [{}, {}]
self.nodes = [self.center]
self.node_set = set(self.nodes)
- self.edges = []
self.ordered_list = None
self.sorted_list = None
+ self.edges = set()
- self.marked = False
-
- """ Static method to load a dgraph from a text
- @param text the saved d-graph
- @param barcode_graph Barcode graph from which the d-graph is extracted
- @return a new d-graph object corresponding to the test
- """
- def load(text, barcode_graph):
+ @staticmethod
+ def load(lcp_txt, variables):
+ """ Static method to load a dgraph from a text
+ :param lcp_txt: the saved d-graph
+ :return: a new d-graph object corresponding to the test
+ """
# basic split
- text = text.replace(']', '')
- _, head, h1, h2 = text.split('[')
+ lcp_txt = lcp_txt.replace(']', '')
+ _, head, h1, h2 = lcp_txt.split('[')
# Head parsing
center = head.replace(' ', '')
- if center not in barcode_graph:
- center = int(center)
dg = Dgraph(center)
# Reload halves
h1 = [x for x in h1.split(',')]
- h1 = [int(x) if x not in barcode_graph else x for x in h1]
h2 = [x for x in h2.split(',')]
- h2 = [int(x) if x not in barcode_graph else x for x in h2]
- dg.put_halves(h1, h2, barcode_graph)
+
+ dg.halves[0] = h1
+ dg.node_set.update(h1)
+ dg.nodes.extend(h1)
+ dg.halves[1] = h2
+ dg.node_set.update(h2)
+ dg.nodes.extend(h2)
return dg
- """ Compute the d-graph quality (score) according to the connectivity between the two halves.
- @param h1 First half of the d-graph
- @param h2 Second half of the d-graph
- @param graph The connectivity graph
- """
def put_halves(self, h1, h2, graph):
+ """ Compute the d-graph quality (score) according to the connectivity between the two halves.
+ :param h1: First half of the d-graph
+ :param h2: Second half of the d-graph
+ :param graph: The barcode graph
+ """
self.score = 0
+ # First half
self.halves[0] = h1
- for node in h1:
- self.node_set.add(node)
- self.nodes.append(node)
+ self.node_set.update(h1)
+ self.nodes.extend(h1)
+ self.connexity[0] = {key: 0 for key in h1}
+ # second half
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.connexity[0] = {key: 0 for key in self.halves[0]}
- self.connexity[1] = {key: 0 for key in self.halves[1]}
- self.edges = []
+ self.node_set.update(h2)
+ self.nodes.extend(h2)
+ self.connexity[1] = {key: 0 for key in h2}
# Compute link arities
for node1 in self.halves[0]:
@@ -76,19 +73,10 @@ class Dgraph(object):
self.connexity[0][node1] += 1
self.connexity[1][node2] += 1
- # Compute links from the center to the other nodes
- for idx, node1 in enumerate(self.nodes):
- for node2 in self.nodes[idx+1:]:
- if graph.has_edge(node1, node2):
- if node1 < node2:
- self.edges.append((node1, node2))
- else:
- self.edges.append((node2, node1))
-
- # Sort the halves by descending connexity
- connex = self.connexity
- self.halves[0].sort(reverse=True, key=lambda v: connex[0][v])
- self.halves[1].sort(reverse=True, key=lambda v: connex[1][v])
+ # Compute covering variable
+ subgraph = graph.subgraph(self.nodes)
+ for _, _, id in subgraph.edges.data("uniq_idx"):
+ self.edges.add(id)
def get_link_divergence(self):
return int(abs(self.score - self.get_optimal_score()))
@@ -104,7 +92,7 @@ class Dgraph(object):
def to_ordered_lists(self):
if self.ordered_list is None:
- hands = [[],[]]
+ hands = [[], []]
for idx in range(2):
prev_connectivity = -1
for node in self.halves[idx]:
diff --git a/deconvolution/main/to_d2_graph.py b/deconvolution/main/to_d2_graph.py
index c7791c903c69effbfbe9e5f9552469ecbc85377b..cb308524c11551dc0e8ef450b81a32677fcc84d0 100755
--- a/deconvolution/main/to_d2_graph.py
+++ b/deconvolution/main/to_d2_graph.py
@@ -8,18 +8,21 @@ from deconvolution.d2graph import d2_graph as d2
def parse_arguments():
- parser = argparse.ArgumentParser(description='Transform a 10X barcode graph into a d2 graph. The program dig for the d-graphs and then merge them into a d2-graph.')
+ parser = argparse.ArgumentParser(description='Transform a barcode graph into a lcp graph. The program dig for a set of lcps and then merge them into a lcp graph.')
parser.add_argument('barcode_graph', help='The barcode graph file. Must be a gefx formated file.')
- parser.add_argument('--output_prefix', '-o', default="d2_graph", help="Output file prefix.")
+ parser.add_argument('--output_prefix', '-o', default="", help="Output file prefix.")
parser.add_argument('--threads', '-t', default=8, type=int, help='Number of thread to use for dgraph computation')
parser.add_argument('--debug', '-d', action='store_true', help="Debug")
parser.add_argument('--verbose', '-v', action='store_true', help="Verbose")
parser.add_argument('--edge_divergence_threshold', '-dt', default=0.25, type=float, help='Divergence threshold value to link two udgs in the d2-graph')
parser.add_argument('--maxclq', '-c', action='store_true', help="Enable max clique community detection (default behaviour)")
parser.add_argument('--louvain', '-l', action='store_true', help="Enable Louvain community detection instead of all max-cliques")
- parser.add_argument('--comtest', '-k', action='store_true', help="Enable [placeholder] community detection algorithm instead of max-cliques")
args = parser.parse_args()
+
+ if args.output_prefix == "":
+ args.output_prefix = ".".join(args.barcode_graph.split(".")[:-1]) + "_lcpg"
+
return args
def main():
@@ -28,26 +31,10 @@ def main():
# debug = args.debug
filename = args.barcode_graph
-
- def dprint(s):
- from datetime import datetime
- t = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
- print(t, s)
-
- dprint("loading barcode graph")
- if filename.endswith('.gexf'):
- G = nx.read_gexf(filename)
- elif filename.endswith('.graphml'):
- G = nx.read_graphml(filename)
- else:
- print("Input file must be gexf or graphml formatted", file=sys.stderr)
- exit(1)
- dprint("barcode graph loaded")
+ barcode_graph = nx.read_gexf(filename)
if args.louvain:
clique_mode = "louvain"
- elif args.comtest:
- clique_mode = "testing"
else:
clique_mode = None
@@ -62,15 +49,15 @@ def main():
shutil.rmtree(debug_path)
os.mkdir(debug_path)
- # Index size must be changed for general purpose. 8 is good for d=5
- dprint("creating D2graph object")
- d2g = d2.D2Graph(G, debug=debug, debug_path=debug_path)
- dprint("D2 graph object created")
- dprint("constructing d2 graph from barcode graph")
- d2g.construct_from_barcodes(neighbor_threshold=args.edge_divergence_threshold, clique_mode=clique_mode, threads=args.threads, verbose=args.verbose)
- dprint("[debug] d2 graph constructed")
-
- # d2g.save(f"{args.output_prefix}.tsv")
+ d2g = d2.D2Graph(debug=debug, debug_path=debug_path)
+ d2g.construct_from_barcodes(
+ barcode_graph,
+ neighbor_threshold=args.edge_divergence_threshold,
+ clique_mode=clique_mode,
+ threads=args.threads,
+ verbose=args.verbose
+ )
+
nx.write_gexf(d2g, f"{args.output_prefix}.gexf")