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

 1 # import os # 导入模块os
 2 import sys # 导入模块sys
 3 f_fasta = sys.argv[1] # 从命令行获取文件名
 4 f = open(f_fasta) # 打开文件
 5 f_RC = open("genome_test_RC.fa","w+")
 6 # 逐行读取
 7 lines = f.readlines()
 8 for line in lines:
 9     line = line.strip() # 去掉行尾的换行符
10     if (line.startswith(">")):
11         chr_id = line + '_RC'
12     else:
13         chr_seq = line[::-1].replace('A','t').replace('T','a').replace('C','g').replace('G','c').upper()
14         # 输出结果
15         print(chr_id)
16         print(chr_seq)
17        
18         f_RC.write(chr_id + '\n') 
19         f_RC.write(chr_seq + '\n') 
20 f.close()
21 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

1 E:\15_python\DEBUG>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