對fasta文件genome_test.fa中的染色體序列進行反向互補，並輸出到文件genome_test_RC.fa

genome_test.fa

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

新疆Reverse_Complement.py文件，並輸入如下python腳本

python腳本

 1 # import os # 導入模塊os
 2 import sys # 導入模塊sys
 3 f_fasta = sys.argv[1] # 從命令行獲取文件名
 4 f = open(f_fasta) # 打開文件
 5 f_RC = open("genome_test_RC.fa","w+")
 6 # 逐行讀取
 7 lines = f.readlines()
 8 for line in lines:
 9     line = line.strip() # 去掉行尾的換行符
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         # 輸出結果
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()

從cmd終端命令行輸入參數，調用上述python腳本，並對genome_test.fa進行處理

1 E:\15_python\DEBUG>python Reverse_Complement.py genome_test.fa

結果

genome_test_RC.fa

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

python學習——讀取染色體長度（七：for循環對染色體序列進行反向互補）