转到字符串中的某个位置 [英] Going to a certain position in a string

问题描述

我想在与我所得到的相反（从负数方面）的字符串上到达某个点。

AAAAAAAAAACCCCCCCCCCCCTTTTTTTTTTGGGGGGGGGG
TTTTTTTTTTGGGGGGGGGGAAAAAAAAAACCCCCCCCCC

因此您需要转换坐标。在底部链上，基数0（最右边的C）与顶部链上的基数39相对。以1为底的是38，以2为底的。（重要点：注意，每次将这两个数相加时会发生什么。）因此，以10为底的是29，以19为底的20。 / p>

因此：如果我想在底部链上找到10-20的底数，我可以在顶部链上找到20-29的底数（然后反向补充）。

我写了以下内容：

  fp = open（infile ，'r'）
 for fp中的行：
 tokens = line.split（）
 exonstarts = tokens [8] [：-1] .split（'，'）
 exonends =令牌[9] [：-1] .split（'，'）
压缩= list（zip（exonstarts，exonends））
 chrom_len = len（chr_string）
s =' '.join（bc [base.upper（）]用于chr_string [-starts-1：-ends-1]中的基数，用于开始，以压缩结尾）+'\n'
  

但是，每次这样做，我都会得到：

错误：全局名称开始'未定义

我该如何解决？

解决方案

尝试在最后一项周围加上括号：

  s =''.join（bc [base.upper（）]为底数（chr_string [-starts-1：-ends-1] \ 
 ^ 
开头，以压缩结尾））+'\n'
 ^ 
  

您在此处定义了两个不同的生成器。这等效于：

  strands =（chr_string [-starts-1：-ends-1]开头，结尾为压缩）
Supplementary_strands =（bc [base.upper（）]为stage_1中的base）
 join_exons =''.join（stage_2）+'\n'
  

I want to get to a certain point on a string that is opposite (from the negative side) to that of what I am given.

AAAAAAAAAACCCCCCCCCCTTTTTTTTTTGGGGGGGGGG TTTTTTTTTTGGGGGGGGGGAAAAAAAAAACCCCCCCCCC

So you need to convert coordinates. On the bottom strand, base 0 (the right-most C) is opposed to base 39 on the top strand. Base 1 is against base 38. Base 2 is against case 37. (Important point: notice what happens when you add these two numbers up — every time.) So base 10 is against base 29, and base 19 is against base 20.

So: if I want to find base 10-20 on the bottom strand, I can look at base 20-29 on the top (and then reverse-complement it).

I have written the following:

fp = open(infile, 'r')
for line in fp:
   tokens = line.split()
   exonstarts = tokens[8][:-1].split(',')
   exonends = tokens[9][:-1].split(',')
   zipped = list(zip(exonstarts, exonends))
   chrom_len = len(chr_string)
   s = ''.join(bc[base.upper()] for base in chr_string[-starts-1:-ends-1] for starts, ends in zipped)+'\n'

Yet, every time I do this I get:

Error: global name 'starts' is not defined

How do I fix this??

解决方案

Try adding parentheses around the last term:

s = ''.join(bc[base.upper()] for base in (chr_string[-starts-1:-ends-1]\
                                         ^
            for starts, ends in zipped)) +'\n'
                                      ^

Your defining two different generators here. This is equivalent to:

strands = (chr_string[-starts-1:-ends-1] for starts, ends in zipped)
complementary_strands = (bc[base.upper()] for base in stage_1)
joined_exons = ''.join(stage_2) + '\n'

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