标签：infinite while-loop loops python
我仍然是一个初学者,因此对于初学者来说,很抱歉这个问题可能有一个明显的答案,而对于混乱的代码很抱歉,但是我有上万行的文件.我正在使用某种窗口框架技术来沿文件滑动,因此我需要确保每个窗口都在其中.但是,我的某些输入文件缺少某些行,因此我尝试用Python编写代码以添加这些行以及我想要的信息,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,就可以正常工作,但情况并非总是如此.在后一种情况下,循环将是无限的.例如,这是输入和所需输出的样子：
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
所需的输出：
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,以使我的这个循环工作而不会无限进行,但我严重看不到我的缺点.有人对我有解决方法的提示吗？
非常感谢您的帮助,在此先感谢您！
解决方法:
尝试以下方法：
#!/usr/bin/python
outfile = open ("missing_test.txt", "w")
def write_line(indiv, window, coverage, snp):
outline = "%s\t%s\t%s\t%s\n" % (indiv, window, coverage, snp)
outfile.write(outline)
with open("add_missing.txt", "r") as file:
lines = file.readlines()
write_line(*lines.pop(0).rstrip().split("\t"))
first_line = lines[0].split("\t")
last_indiv = first_line[0]
last_window = int(first_line[1])
for line in lines:
indiv, window, coverage, snp = line.split("\t")
window = int(window)
coverage = int(coverage)
snp = int(snp)
if indiv == last_indiv:
# If the current window is higher than expected,
# insert a line with the missing window.
# Repeat until we get to the expected window.
while window > last_window + 10000:
write_line(indiv, last_window + 10000, coverage, 0)
last_window += 10000
last_window = window
else:
last_indiv = indiv
last_window = window
write_line(indiv, window, coverage, snp)
它不包含的是期望某个窗口号是给定indiv中的第一个窗口,因为您没有定义该行为,并且对此的评论相当混乱.
运行此脚本后,missing_test.txt的内容：
06001
标签：infinite,while-loop,loops,python 来源： https://codeday.me/bug/20191111/2022644.html
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