Python|将CDS序列转为PEP序列

  有蛋白编码基因的核苷酸序列，想要转化成对应的氨基酸序列，可以利用Python的Biopython Module来实现。

1. 提取核苷酸序列信息

  原始的保存着核苷酸序列的fasta文件里还有着序列的id等说明信息，我们只需要核苷酸序列，可以用for循环遍历每一行，将偶数行输出到一个新的文本文档中。

# opening the file
file1 = open('D:/.../PCGs/cytb/cytb.fas', 'r')

# creating another file to store even lines
file2 = open('D:/.../PCGs/cytb/cytb_no_label.fas', 'w')

# reading content of the files and writing even lines to another file
lines = file1.readlines()

for i in range(0, len(lines)):
    if (i % 2 != 0):
        file2.write(lines[i])

# closing the files
file1.close()
file2.close()

2. 利用Biopython将CDS转为PEP

#importing the Biopython package 
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC

#opening the file
file1 = open('D:/.../PCGs/atp6/atp6_no_label.fas')
file2 = open('D:/.../PCGs/atp6/atp6_aa_no_label.fas', 'w'