1

我是一名业余程序员（我的实际专业是生物学），所以如果代码很糟糕，我深表歉意。

无论如何，我正在做一个 rosalind.info 练习（http://rosalind.info/problems/subs/），希望我找到一个特定 DNA 基序包含在更大 DNA 序列中的每个索引。基本上，我需要在字符串中找到子字符串的索引。应该很容易吧？好吧，也许你可以帮助我。

所以这是我的代码：

with open('rosalind_subs.txt') as f:
    seq = f.readline()
    seq.strip()
    subs = f.readline()
    subs.strip()
    break

def finder(x, y):
    index = x.find(y)
    return index

print("sequence is: " + seq)
print("subs is: " + subs)

print(finder(seq, subs))

这是我的输出：

sequence is:  ACCAGTCTCTTTTTTCTCTTTTCTCTTTTCTCTTTTGACCCTCTTTTCGTCACTCTTTTACCTCTTTTTCTCTTTTACTCTTTTCTCTTTTACTCTTTTACTCTTTTAGCGCAGATCTCTTTTCTCTTTTGGCTCTTTTGTCATCCTCTTTTAGACTCTTTTGGGAAGCGACGCCTCTTTTCTCTTTTCTCTTTTGCCTCTTTTTATAACCTAAAAGACTCTTTTCCCTCTTTTCCGATTTGCCAAGGGCTCTCTTTTCTCTTTTGCTCTTTTCTCTTTTCTCTTTTTACTCTTTTCTCTTTTCGCCCCAAGATTAACTCTTTTTCTCTTTTCTCTCTTTTTTCCTCTTTTCTCTTTTGAATTGACCTCTTTTTCTCTTTTTTTGGGCCGCTCTTTTCTCTTTTACTCTTTTCTCTCTTTTAACAGCTCTTTTCCTTCTCTTTTGTCTCTTTTAGTATACTCTTTTACTCTTTTCTCTTTTCTCTCTTTTACTCTTTTGCTCTTTTCTCTTTTTGTCTCTTTTGCCCTGTCTCTTTTCACGCTTCTCTTTTAGTGTACTCTTTTACTCTTTTTGGCTCTTTTCGAATTTGTTAGCTCTTTTGCTCTTTTCTCTTTTGCTCTTTTGTCTCTTTTGATCAGATTCTCTTTTTCTCTTTTCTCTTTTCCTTAAGCAGATTTCTCTTTTCTCTTTTTCTCTCTTTTGCTCTTTTACTCTTTTACTGCTTTCTCTTTTACAACCTCTTTTACTCTTTTAAGCTCTTTTCTCTTTTGCGCCTCTTTTCCTCCCCTCTTTTTAGCTCTTTTCTCTTTTTCGCTCTTTTCAGCTCTTTTCACTCTTTTGTTTTGAGCTCTTTTCAGACTCTTTTATCCTCTTTTTTCCTCTTTTAGCGCTCTTTTGTAGCCTCTTTT

motif is: CTCTTTTCT

-1

***Repl Closed***

我把它***Repl Closed***留在那里，努力不遗余力。也许它与 Sublime REPL 有关？

无论如何，您可能无法仅通过查看来判断，但实际上在 DNA 序列中多次发现该基序，只是查找功能没有发现它。是什么赋予了？

4

2 回答 2

1

break 不适用于 with 范围。请删除并尝试。我已经测试了下面的代码。

with open('rosalind_subs.txt') as f:
    seq = f.readline()
    seq.strip()
    subs = f.readline()
    subs.strip()

def finder(x, y):
    index = x.find(y)
    return index

print("sequence is: " + seq)
print("subs is: " + subs)

print(finder(seq, subs))

输出是

>>> 
sequence is: ACCAGTCTCTTTTTTCTCTTTTCTCTTTTCTCTTTTGACCCTCTTTTCGTCACTCTTTTACCTCTTTTTCTCTTTTACTCTTTTCTCTTTTACTCTTTTACTCTTTTAGCGCAGATCTCTTTTCTCTTTTGGCTCTTTTGTCATCCTCTTTTAGACTCTTTTGGGAAGCGACGCCTCTTTTCTCTTTTCTCTTTTGCCTCTTTTTATAACCTAAAAGACTCTTTTCCCTCTTTTCCGATTTGCCAAGGGCTCTCTTTTCTCTTTTGCTCTTTTCTCTTTTCTCTTTTTACTCTTTTCTCTTTTCGCCCCAAGATTAACTCTTTTTCTCTTTTCTCTCTTTTTTCCTCTTTTCTCTTTTGAATTGACCTCTTTTTCTCTTTTTTTGGGCCGCTCTTTTCTCTTTTACTCTTTTCTCTCTTTTAACAGCTCTTTTCCTTCTCTTTTGTCTCTTTTAGTATACTCTTTTACTCTTTTCTCTTTTCTCTCTTTTACTCTTTTGCTCTTTTCTCTTTTTGTCTCTTTTGCCCTGTCTCTTTTCACGCTTCTCTTTTAGTGTACTCTTTTACTCTTTTTGGCTCTTTTCGAATTTGTTAGCTCTTTTGCTCTTTTCTCTTTTGCTCTTTTGTCTCTTTTGATCAGATTCTCTTTTTCTCTTTTCTCTTTTCCTTAAGCAGATTTCTCTTTTCTCTTTTTCTCTCTTTTGCTCTTTTACTCTTTTACTGCTTTCTCTTTTACAACCTCTTTTACTCTTTTAAGCTCTTTTCTCTTTTGCGCCTCTTTTCCTCCCCTCTTTTTAGCTCTTTTCTCTTTTTCGCTCTTTTCAGCTCTTTTCACTCTTTTGTTTTGAGCTCTTTTCAGACTCTTTTATCCTCTTTTTTCCTCTTTTAGCGCTCTTTTGTAGCCTCTTTT

subs is: CTCTTTTCT
15
于 2015-11-26T14:21:57.680 回答
0

也是一位在这里做过几次 rosalind.info 练习的生物学家。

首先，可以通过使用来改进要读取序列和主题的代码splitlines()，它负责删除换行符。还要注意我如何使用元组解包来同时分配seq和motif变量。

with open('rosalind_subs.txt') as f:
    seq, motif = f.read().splitlines()

接下来，您正确地注意到find它只返回您的主题第一次出现的索引。要查找所有出现的情况，知道 find 需要另一个可选参数会有所帮助start。如果您提供它，它将从该索引位置开始查找。在循环中使用它，您将获得所有索引。

另一种方法是使用正则表达式。请注意，主题可能会相互重叠，因此您需要使用前瞻断言。

于 2015-11-26T15:00:32.423 回答