python 计算 fastq数据中的GC 含量

 

001、

(base) [b20223040323@admin1 test]$ ls
SRR1770413_1.fastq  SRR1770413_2.fastq  test.py
(base) [b20223040323@admin1 test]$ cat test.py
#!/bin/env python
# -*- coding:utf-8 -*-

from Bio import SeqIO

fq1 = list(SeqIO.parse("SRR1770413_1.fastq", "fastq"))
fq2 = list(SeqIO.parse("SRR1770413_2.fastq", "fastq"))

total_gc = 0
total_bases = 0

for i in fq1:
        i = str(i.seq)
        total_gc += i.count('G') + i.count('C') + i.count('g') + i.count('c')
        total_bases += len(i)
for i in fq2:
        i = str(i.seq)
        total_gc += i.count('G') + i.count('C') + i.count('g') + i.count('c')
        total_bases += len(i)

print("GC_count:" + str(total_gc/total_bases))

(base) [b20223040323@admin1 test]$ python test.py
GC_count:0.6710963455149501

 。

 

更正一下，python脚本的解释器写错了，正确的应该为：

#！/usr/bin/env python

# -*- coding:  uft-8 -*-