将字节类型文件转换为 python 中的可用格式

Question

I have to read the table in below link(html page) into a dict() and then work on it. However, with the below code I gave, the table still looks clumsy and I do not understand from where to start working to make it a dictionary of codon sequence(eg AGU) to respective Amino Acid. Any way to make it look better? May be something like a DataFrame or any other suggestions? Please help. Thanks.

link = "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=N"
f = urllib.request.urlopen(link)
myfile = f.read()
s = myfile.decode()
s.strip(" ")

Answer 1

If you have looked at the page http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=N you would have noticed that it contains not just the codon sequence you want, but a lot of HTML around it. To extract just the codons, the best way is likely to use BeautifulSoup:

from bs4 import BeautifulSoup
link = "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606&aa=1&style=N"
f = urllib.request.urlopen(link)
myfile = f.read()
s = myfile.decode()
codons = BeautifulSoup(s).find('pre').text

Now you should probably process this string further to get the form you want - dict, list, dataframe, whatever. Assuming you just want a dict, since you mentioned a dictionary:

import re
codons_dict = { t[0]: t[1] for t in sorted(re.findall(r'(\w{3})\s+\w\s+(\S+)\s+\S+\s+[(]\d+[)]', codons)) }