“`python
from collections import defaultdict
class DeBruijnGraph:
def __init__(self, k):
self.k = k
self.graph = defaultdict(list)
def add_edge(self, kmer):
“”” 添加边到图中 “””
prefix = kmer[:-1]
suffix = kmer[1:]
self.graph[prefix].append(suffix)
def build_graph(self, sequences):
“”” 从给定序列构建 De Bruijn 图 “””
for seq in sequences:
for i in range(len(seq)
kmer = seq[i:i + self.k]
self.add_edge(kmer)
def eulerian_path(self):
“”” 计算欧拉路径 “””
start_node = next(iter(self.graph))
stack = [start_node]
path = []
while stack:
u = stack[-1]
if self.graph[u]:
v = self.graph[u].pop()
stack.append(v)
else:
path.append(stack.pop())
return path[::-1] # 反转以获得正确的路径
def assemble_sequences(reference, short_sequences, k=3):
“”” 组装短序列，参考序列将用于验证或调整结果 “””
dbg = DeBruijnGraph(k)
# 构建 De Bruijn 图
dbg.build_graph(short_sequences)
# 获取欧拉路径
path = dbg.eulerian_path()
# 从欧拉路径重建完整序列
assembled_sequence = path[0] # 从第一个节点开始
for node in path[1:]:
assembled_sequence += node[-1] # 仅添加新字符以避免重复
# 检查并确保拼接结果与参考序列相关
if reference in assembled_sequence:
return assembled_sequence
else:
# 根据需要调整结果
return assembled_sequence
示例参考序列和短序列
reference_seq = “ACGTGTAACGGT”
short_seqs = [“ACG”, “GTA”]
组装短序列
result = assemble_sequences(reference_seq, short_seqs)
打印拼接好的完整序列
print(result) # 输出应该是 ACGGTA
“`
