Python 官方文档:入门教程 => 点击学习
目录前言问题思路1. 预处理2. 将pretreatment.txt作为输入文件,3.去重+归并排序4.开始比对,gap=505.将new_result.txt作为输出文件,生成结果
RepeatMasker是一个通过已有数据库预测重复序列的软件,可以筛选DNA序列中的散在重复序列和低复杂序列,是重复序列注释的重要软件。
我们想对RepeatMasker预测的结果文件进行重复序列的合并,也就是去除染色体之间的overlap区域同时将基因间距小于50个bp的也同样视为overlap,我们应该如何用python处理并生成新的预测结果?
我们这里只需要结果文件的前三列,可以使用awk命令获取
awk '{for(i = 1; i <= 3; i++)
printf("%s ", $i);
printf("\n")}' result.txt > pretreatment.txt
#result.txt为结果文件,pretreatment.txt为预处理结果文件
with open ('pretreatment.txt','r')as f:
for i in f.readlines():
if i.strip() == '//':
continue
c = i.strip().split('\t')
b.append(c[0])
a.append((c[0],int(c[1]),int(c[2])))
print ("全部染色体数量: "+str(len(a)))
c = [i for i in b_set if b.count(i) == 1]
for i in a:
if i[0] not in c:
continue
a.remove(i)
result.append((i[0],int(i[1]),int(i[2])))
print ("去重后染色体数量: "+str(len(a)))
a.sort(key = lambda x : (x[0], x[1], x[2]))
#按照第一列,第二列,第三列分别排降升序
q = ''
start = 0
end = 0
tem1 = []
tem2 = []
gap = 50
for i in a:
if i[0] != q:
if tem1:
if tem1 not in tem2:
tem2.append(tem1)
tem1 = []
q = I[0]
start = int(i[1])
end = int(i[2])
continue
if int(i[1]) < end or int(i[1]) - end < gap:
if int(i[2]) > end:
end = int(i[2])
continue
else:
continue
tem1.append([q,start,end])
start = int(i[1])
end = int(i[2])
with open ('new_result.txt','w')as f:
for i in tem2:
for o in I:
print (o[0],o[1],o[2],file=f)
for i in result:
print (i[0],i[1],i[2],file=f)
a = []
b = []
with open ('pretreatment.txt','r')as f:
for i in f.readlines():
if i.strip() == '//':
continue
c = i.strip().split('\t')
b.append(c[0])
a.append((c[0],int(c[1]),int(c[2])))
print ("全部染色体数量: "+str(len(a)))
b_set = set(b)
result = []
c = [i for i in b_set if b.count(i) == 1]
for i in a:
if i[0] not in c:
continue
a.remove(i)
result.append((i[0],int(i[1]),int(i[2])))
print ("去重后染色体数量: "+str(len(a)))
a.sort(key = lambda x : (x[0], x[1], x[2]))
q = ''
start = 0
end = 0
tem1 = []
tem2 = []
gap = 50
for i in a:
if i[0] != q:
if tem1:
if tem1 not in tem2:
tem2.append(tem1)
tem1 = []
q = I[0]
start = int(i[1])
end = int(i[2])
continue
if int(i[1]) < end or int(i[1]) - end < gap:
if int(i[2]) > end:
end = int(i[2])
continue
else:
continue
tem1.append([q,start,end])
start = int(i[1])
end = int(i[2])
with open ('new_result.txt','w')as f:
for i in tem2:
for o in I:
print (o[0],o[1],o[2],file=f)
for i in result:
print (i[0],i[1],i[2],file=f)
以上就是Python合并RepeatMasker预测结果中染色体的overlap区域的详细内容,更多关于python RepeatMasker预测overlap的资料请关注编程网其它相关文章!
--结束END--
本文标题: python合并RepeatMasker预测结果中染色体的overlap区域
本文链接: https://www.lsjlt.com/news/119059.html(转载时请注明来源链接)
有问题或投稿请发送至: 邮箱/279061341@qq.com QQ/279061341
下载Word文档到电脑,方便收藏和打印~
2024-03-01
2024-03-01
2024-03-01
2024-02-29
2024-02-29
2024-02-29
2024-02-29
2024-02-29
2024-02-29
2024-02-29
回答
回答
回答
回答
回答
回答
回答
回答
回答
回答
0