fam_to_graph.py 文件源码

def processFeatures(self):
        sys.stderr.write("parsing features and constructing kmer graph\n")  
        kmer_q=deque()
        prev_feature=None
        #loop through figfams to create kmers
        repeat_num=1
        update_repeats=[]
        for feature in self.feature_parser.parse():
            if prev_feature and prev_feature.group_id == feature.group_id and prev_feature.contig_id == feature.contig_id:
                repeat_num+=1
                update_repeats.append(prev_feature)
                if self.eat_repeats:
                    continue
            else:
                if repeat_num >1:
                    update_repeats.append(prev_feature)
                    for to_up in update_repeats:
                        to_up.repeat_num =repeat_num
                repeat_num=1
                update_repeats=[]
            feature.feature_id= len(self.feature_index)
            self.feature_index.append(feature)
            if prev_feature == None or prev_feature.genome_id != feature.genome_id:
                self.trackDiversity(feature.feature_id, self.all_diversity)
            if feature.genome_id not in self.replicon_map:
                self.replicon_map[feature.genome_id]=set()
            else:
                self.replicon_map[feature.genome_id].add(feature.contig_id)
            if(prev_feature and prev_feature.contig_id != feature.contig_id):
                kmer_q=deque()#clear kmer stack because switching replicons
                self.prev_node=None
                self.prev_indices=[]
            elif prev_feature and prev_feature.contig_id == feature.contig_id:
                if prev_feature.start > feature.start:
                    assert InputError
            #depending on the context populate the context bin with appropriate ids to detect duplicates
            if self.context:
                if(prev_feature and prev_feature.getContextValue(self.context) != feature.getContextValue(self.context)):
                    self.context_bin.clear()
            kmer_q.append(feature)#append the feature to the queue
            if(len(kmer_q)>self.ksize):
                kmer_q.popleft()
                self.addRFNode(kmer_q)
            elif(len(kmer_q)== self.ksize):
                self.addRFNode(kmer_q)#right now only passing in the last figfams information
            else:#kmer size is less than ksize
                kmer=None
            prev_feature=feature
        if self.debug: nx.set_node_attributes(self.rf_graph, "visit", "")