python学习——读取染色体长度（七：for循环对染色体序列进行反向互补）

对fasta文件genome_test.fa中的染色体序列进行反向互补，并输出到文件genome_test_RC.fa

genome_test.fa

>chr1
ATATATATAT
>chr2
ATATATATATCGCGCGCGCG
>chr3
ATATATATATCGCGCGCGCGATATATATAT
>chr4
ATATATATATCGCGCGCGCGATATATATATCGCGCGCGCG
>chr5
ATATATATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATAT

新疆Reverse_Complement.py文件，并输入如下python脚本

python脚本

# import os # 导入模块os
import sys # 导入模块sys
f_fasta = sys.argv[1] # 从命令行获取文件名
f = open(f_fasta) # 打开文件
f_RC = open("genome_test_RC.fa","w+")
# 逐行读取
lines = f.readlines()
for line in lines:
    line = line.strip() # 去掉行尾的换行符
    if (line.startswith(">")):
        chr_id = line + '_RC'
    else:
        chr_seq = line[::-1].replace('A','t').replace('T','a').replace('C','g').replace('G','c').upper()
        # 输出结果
        print(chr_id)
        print(chr_seq)
       
        f_RC.write(chr_id + '
') 
        f_RC.write(chr_seq + '
') 
f.close()
f_RC.close()

从cmd终端命令行输入参数，调用上述python脚本，并对genome_test.fa进行处理

E:15_pythonDEBUG>python Reverse_Complement.py genome_test.fa

结果

genome_test_RC.fa

>chr1_RC
ATATATATAT
>chr2_RC
CGCGCGCGCGATATATATAT
>chr3_RC
ATATATATATCGCGCGCGCGATATATATAT
>chr4_RC
CGCGCGCGCGATATATATATCGCGCGCGCGATATATATAT
>chr5_RC
ATATATATATCGCGCGCGCGATATATATATCGCGCGCGCGATATATATAT