Extraction.py 文件源码

def __loadGMLFiles__(self):
        """
        Iterates through all of the files inside of support directory
        merges these graphs with the whole gapGraph
        creates a dictionary of {"readName":[gapName or nodeName,...] }
        """
        self.readSupport = defaultdict(list)
        for i in glob.glob(os.path.join(self.protocol.outDir,"support","*.gml")):
            truncNxVer = float('.'.join(networkx.__version__.split('.')[:2]))
            if truncNxVer >= 1.7:
                try:
                    inputGml = networkx.read_gml(i, relabel=True)
                except ValueError:
                    logging.warning("GML file %s is empty" % i)
                    continue
            elif truncNxVer == 1.1:
                inputGml = networkx.read_gml(i)
            else:
                logging.warning("It is unknown if networkx version %s will work." % networkx.__version__)
                logging.warning("If you get an error here, please report it!!!")
                inputGml = networkx.read_gml(i)

            for node in inputGml.nodes_iter():
                for readName in inputGml.node[node]['extenders'].split(':'):
                    if readName == '':
                        continue
                    trimInfo = self.__cleanReadName__(readName)
                    self.gapGraph.add_extend(node, trimInfo.name)
                    self.readSupport[trimInfo.name].append((node, trimInfo))

            for source, target, evidence in inputGml.edges_iter(data=True):
                for readName in evidence['evidence'].split(':'):
                    if readName == '':
                        continue
                    trimInfo = self.__cleanReadName__(readName)
                    self.gapGraph.add_evidence(source, target, trimInfo.name)
                    self.readSupport[trimInfo.name].append((source, target, trimInfo))
        self.readSupport = dict(self.readSupport)