python 中统计fastq文件中 GC含量

 

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")
idx = 0
str1 = ""

for i in in_file:
    idx += 1
    i = i.strip()
    if idx % 4 == 2:
        str1 += i

gc = str1.count("G") + str1.count("C")
out_file.write(str(gc/len(str1)) + "\n")

in_file.close()
out_file.close()
root@PC1:/home/test# python test.py                              ## 运行程序
root@PC1:/home/test# ls
a.fastq  result.txt  test.py
root@PC1:/home/test# cat result.txt                              ## 运行结果
0.49038461538461536

 

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