ComplexResolver.py 文件源码

def makeClusters(self, chrom):
        """
        yield all non-solo clusters
        returns all of the BreakPoints that comprise the events within the
        cluster
        """
        #PARAM
        MAXSPAN = self.maxSpan
        MAXOVLS = self.maxOvl

        intervalTree = self.genome[chrom]
        overlaps = []

        graph = nx.Graph()
        #Find clusters on the chromosome
        #By building a graph
        for interval in intervalTree:
            if abs(interval.end - interval.begin) > MAXSPAN:
                continue
            ovls = intervalTree.search(interval)
            if len(ovls) == 1 or len(ovls) > MAXOVLS:
                continue
            for a,b in itertools.combinations(ovls, 2):
                if abs(a.end - a.begin) > MAXSPAN \
                   or abs(b.end - b.begin) > MAXSPAN:
                    continue
                graph.add_edge(a, b)

        #clusters are sub graphs
        for subG in nx.connected_component_subgraphs(graph):
            if len(subG.edges()) == 0:
                continue

            lookup = [x.data for x in subG.nodes()]
            ret = [x for x in self.points[chrom] if x.id in lookup]

            #I need to merge points that are too close

            if len(ret) <= 10:
                yield ret