更新网络状态是什么意思
时间: 2023-09-18 20:13:25 浏览: 36
当然可以,以下是一个可能的实现:
```python
from collections import defaultdict
# 读取bed文件并记录SMNDC1和snoRNA的地点
SMNDC1_locs = defaultdict(list)
snoRNA_locs = defaultdict(list)
with open("HepG2_SMNDC1_Ctrl_snoRNA_intersect_sorted.bed") as f:
for line in f:
parts = line.strip().split("\t")
chrom, start, end, name, score, strand = parts[:6]
if name.startswith("SMNDC1"):
SMNDC1_locs[(chrom, strand)].append((int(start), int(end)))
elif name.startswith("snoRNA"):
snoRNA_locs[(chrom, strand)].append((int(start), int(end)))
# 找到SMNDC1在snoRNA上下游50bp内的位置
upstream_dict = defaultdict(list)
downstream_dict = defaultdict(list)
for (chrom, strand), SMNDC1_list in SMNDC1_locs.items():
for (sm_start, sm_end) in SMNDC1_list:
for (sn_start, sn_end) in snoRNA_locs[(chrom, strand)]:
if strand == "+":
if sm_end + 50 >= sn_start and sm_end < sn_start:
upstream_dict[(chrom, strand)].append((sn_start - 50, sn_start, sm_start, sm_end))
elif sn_end <= sm_start + 50 and sn_end > sm_start:
downstream_dict[(chrom, strand)].append((sn_end, sn_end + 50, sm_start, sm_end))
else:
if sn_end + 50 >= sm_start and sn_end < sm_start:
upstream_dict[(chrom, strand)].append((sn_end, sn_end + 50, sm_start, sm_end))
elif sm_end <= sn_start + 50 and sm_end > sn_start:
downstream_dict[(chrom, strand)].append((sn_start, sn_start - 50, sm_start, sm_end))
# 输出结果
for (chrom, strand), sm_list in upstream_dict.items():
with open(f"{chrom}_{strand}_upstream.bed", "w") as f:
for loc in sm_list:
f.write(f"{chrom}\t{loc[2]}\t{loc[3]}\t{chrom}:{loc[0]}-{loc[1]}\n")
for (chrom, strand), sm_list in downstream_dict.items():
with open(f"{chrom}_{strand}_downstream.bed", "w") as f:
for loc in sm_list:
f.write(f"{chrom}\t{loc[2]}\t{loc[3]}\t{chrom}:{loc[0]}-{loc[1]}\n")
```
这个脚本读取bed文件并将SMNDC1和snoRNA的位置信息记录在字典中。然后它将SMNDC1和snoRNA的组合与snoRNA区域中的位置相比较,以找到在上游或下游50bp内的SMNDC1。最后,它将这些位置写入文件中,文件名包括染色体号和链号。注意,这个脚本假设输入的bed文件已经经过排序并且没有重复项。
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