我仍然是一个初学者,所以对于初学者来说,很抱歉这个问题可能有一个明显的答案,也很抱歉代码混乱,但我有上万行的文件。我正在使用一种特定的窗口框架技术来滑动我的文件,所以我需要确保每个窗口都在那里。但是,我的一些输入文件遗漏了某些行,因此我尝试用Python编写代码来添加这些行和我想要的信息,以使文件完整。代码如下所示:
#!/usr/bin/env python
outfile = open ("missing_test.txt", "w")
with open("add_missing.txt", "r") as file:
last_line = 0 #This is where it starts for bin 1
lines = []
header_line = next(file)
outfile.write(header_line)
CHROM = 'BABA_1'
for line in file: #go through every line to check its existence and rewrite to new file
nums = line.split("\t")
num1 = nums[0] #no integer because this is a string: name individual
num2 = int(nums[1]) #integer for window
num3 = int(nums[2]) #integer for coverage (here always 10000 to met treshold)
num4 = int(nums[3]) #integer for SNP count
if num1 == CHROM: #
while num2 != last_line + 10000:
#A line is missing, so a new line is added with 0 SNPs:
NUM2 = last_line + 10000 # New window, the one that was missing
NUM4 = 0 #0 SNPs found
#lines.append((num1, NUM2, num3, NUM4))
OUTLINE = "%s\t%s\t%s\t%s" % (num1, NUM2, num3, NUM4) #write new line to outfile
outfile.write(OUTLINE + "\n")
last_line += 10000
lines.append((num1,num2,num3,num4))
last_line += 10000 #also add 10000 here otherwise the while loop makes no sense
outline = "%s\t%s\t%s\t%s" % (num1, num2, num3, num4)
outfile.write(outline + "\n") #write all existing lines to outfile
else:
CHROM = num1
last_line = 0
outfile.close()
因此,只要第一个“CHROM”的第一个窗口等于0,就可以很好地工作,但情况并非总是这样。在后一种情况下,循环将是无限的。例如,输入和期望输出如下所示:
输入:
indiv window coverage SNP
BABA_1 20000 10000 7
BABA_1 30000 10000 1
BABA_1 50000 10000 2
BABA_1 60000 10000 3
BABA_1 80000 10000 1
BABA_10 20000 10000 1
BABA_10 30000 10000 16
BABA_10 80000 10000 9
期望输出:
indiv window coverage SNP
BABA_1 10000 10000 0
BABA_1 20000 10000 7
BABA_1 30000 10000 1
BABA_1 40000 10000 0
BABA_1 50000 10000 2
BABA_1 60000 10000 3
BABA_1 70000 10000 0
BABA_1 80000 10000 1
BABA_10 10000 10000 0
BABA_10 20000 10000 1
BABA_10 30000 10000 16
BABA_10 40000 10000 0
BABA_10 50000 10000 0
BABA_10 60000 10000 0
BABA_10 70000 10000 0
BABA_10 80000 10000 9
我一直在努力寻找答案,以得到这个虽然我的循环工作没有无限,但我真的没有看到我的缺陷。有没有人能告诉我怎么解决这个问题?你知道吗
非常感谢您的帮助,提前谢谢!你知道吗
您可以使用以下方法,首先构建一个空列表,然后将任何现有条目分配到其中,然后再将它们作为行写入输出:
给你:
试着按照这些思路来做:
它没有包含的是某个窗口号在给定的
indiv
中是第一个的期望,因为您没有定义该行为,而且您对此的评论相当混乱。你知道吗缺失内容_测试.txt运行此脚本后:
相关问题 更多 >
编程相关推荐