python 中实现将fastq文件转换为fasta文件

 

001、

root@PC1:/home/test# ls
a.fastq  test.py
root@PC1:/home/test# cat a.fastq                                     ## 测试fastq文件
@DJB775P1:248:D0MDGACXX:7:1202:12362:49613
TGCTTACTCTGCGTTGATACCACTGCTTAGATCGGAAGAGCACACGTCTGAA
+
JJJJJIIJJJJJJHIHHHGHFFFFFFCEEEEEDBD?DDDDDDBDDDABDDCA
@DJB775P1:248:D0MDGACXX:7:1202:12782:49716
CTCTGCGTTGATACCACTGCTTACTCTGCGTTGATACCACTGCTTAGATCGG
+
IIIIIIIIIIIIIIIHHHHHHFFFFFFEECCCCBCECCCCCCCCCCCCCCCC
root@PC1:/home/test# cat test.py                                    ## 测试程序
#!/usr/bin/python
in_file = open("a.fastq", "r")
out_file = open("result.txt", "w")
dict1 = {}
idx = 0

for i in in_file:
    idx = idx + 1
    i = i.strip()
    if idx % 4 == 1:
        key = "".join(i.split("@")[1:])
        dict1[key] = ""
    elif idx % 4 == 2:
        dict1[key] = i
for i,j in dict1.items():
    print(">{0}\n{1}".format(i,j), file = out_file)

in_file.close()
out_file.close()
root@PC1:/home/test# python test.py                                         ## 执行程序
root@PC1:/home/test# ls
a.fastq  result.txt  test.py
root@PC1:/home/test# cat result.txt                                         ## 执行程序结果
>DJB775P1:248:D0MDGACXX:7:1202:12362:49613
TGCTTACTCTGCGTTGATACCACTGCTTAGATCGGAAGAGCACACGTCTGAA
>DJB775P1:248:D0MDGACXX:7:1202:12782:49716
CTCTGCGTTGATACCACTGCTTACTCTGCGTTGATACCACTGCTTAGATCGG

参考：https://www.jianshu.com/p/5ee54bea4cb0