process.py 文件源码

def dump(self):
        '''
        write the current state to file
        '''
        self.log.warn("unsure if dump() works")
        from cPickle import dump
        from Bio import Phylo
        for attr_name, fname in self.file_dumps.iteritems():
            if hasattr(self,attr_name):
                print("dumping",attr_name)
                #if attr_name=='seqs': self.seqs.all_seqs = None
                with myopen(fname, 'wb') as ofile:
                    if attr_name=='nodes':
                        continue
                    elif attr_name=='tree':
                        #biopython trees don't pickle well, write as newick + node info
                        self.tree.dump(fname, self.file_dumps['nodes'])
                    else:
                        dump(getattr(self,attr_name), ofile, -1)