我有两个bed文件,一个是snoRNA的bed文件,一个是某一个RBP(RNA结合蛋白)的bed文件,现在我需要写一个脚本来以这两个文件为输入,来分析该RBP在snoRNA上下游(50bp)的覆盖信号,你能写出这样的脚本么?
时间: 2024-05-07 22:16:00 浏览: 14
是的,可以写一个Python脚本来实现这个功能。以下是一个示例脚本,它假设输入的bed文件已经按照染色体和坐标进行了排序。
```python
import argparse
parser = argparse.ArgumentParser(description='Calculate coverage of an RBP on snoRNAs')
parser.add_argument('snoRNA_bed', help='bed file of snoRNAs')
parser.add_argument('rbp_bed', help='bed file of RBP binding sites')
parser.add_argument('--upstream', type=int, default=50, help='number of bp upstream of snoRNAs to consider')
parser.add_argument('--downstream', type=int, default=50, help='number of bp downstream of snoRNAs to consider')
args = parser.parse_args()
# read in snoRNA bed file
snoRNAs = {}
with open(args.snoRNA_bed, 'r') as f:
for line in f:
fields = line.strip().split('\t')
chrom, start, end, name = fields[0], int(fields[1]), int(fields[2]), fields[3]
snoRNAs[name] = (chrom, start, end)
# read in RBP bed file
rbp_sites = []
with open(args.rbp_bed, 'r') as f:
for line in f:
fields = line.strip().split('\t')
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
rbp_sites.append((chrom, start, end))
# calculate coverage of RBP on snoRNAs
for name, (chrom, start, end) in snoRNAs.items():
upstream_start = max(0, start - args.upstream)
downstream_end = end + args.downstream
snoRNA_length = downstream_end - upstream_start
# calculate coverage
coverage = 0
for rbp_chrom, rbp_start, rbp_end in rbp_sites:
if rbp_chrom == chrom and rbp_start <= downstream_end and rbp_end >= upstream_start:
overlap_start = max(rbp_start, upstream_start)
overlap_end = min(rbp_end, downstream_end)
overlap_length = overlap_end - overlap_start
coverage += overlap_length
coverage = coverage / snoRNA_length
print(name, coverage)
```
这个脚本使用argparse模块来处理命令行参数,接受两个bed文件的路径以及上下游范围。它首先读入snoRNA的bed文件,将snoRNA的名称作为键,将染色体和坐标作为值存储在字典中。然后它读入RBP的bed文件,将每个结合位点的染色体和坐标存储在一个列表中。接下来,对于每个snoRNA,它计算其上下游范围,将其长度用于计算覆盖率。它然后遍历RBP结合位点列表,找到与snoRNA重叠的结合位点,并计算它们的重叠长度。最后,它将所有的重叠长度加起来,并除以snoRNA的长度,得到覆盖率。最后,它将snoRNA的名称和覆盖率输出到标准输出中。