我正在尝试在 python 中编写代码,以帮助我在两个特定字符串之间查找字符串。当我用单个字符串实现代码时,我得到了所需的输出。但是,我需要匹配序列数组中的模式。它一直给我一个错误。
定义一个函数来查找两个用户指定序列之间的模式:
import re
def find_between(prefix, suffix, text):
pattern = r"{}\s*(.*)\s*{}".format(re.escape(prefix), re.escape(suffix))
result = re.search(pattern, text, re.DOTALL)
if result:
return result.group(1)
else:
return None
当我尝试单个字符串时,它可以工作:
text = "AGGTCCTGTAAACCT"
prefix = "TCCT"
suffix = "ACCT"
find_between(prefix, suffix, text)
输出:'GTAA'
但是当我尝试读取 fastq 文件并实现搜索时,它不会:
seqs = readFastq('FN1.fastq')
text = seqs
prefix = "TCCT"
suffix = "ACCT"
find_between(prefix, suffix, text)
它向我抛出了这个错误
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-26-9c35672e7561> in <module>()
2 prefix = "TCCT"
3 suffix = "ACCT"
----> 4 find_between(prefix, suffix, text)
<ipython-input-19-5f42599c717f> in find_between(prefix, suffix, text)
3 def find_between(prefix, suffix, text):
4 pattern = r"{}\s*(.*)\s*{}".format(re.escape(prefix), re.escape(suffix))
----> 5 result = re.search(pattern, text, re.DOTALL)
6 if result:
7 return result.group(1)
/Users/shravantikrishna/anaconda/lib/python3.6/re.py in search(pattern, string, flags)
180 """Scan through string looking for a match to the pattern, returning
181 a match object, or None if no match was found."""
--> 182 return _compile(pattern, flags).search(string)
183
184 def sub(pattern, repl, string, count=0, flags=0):
TypeError: expected string or bytes-like object