python 计算 fastq数据中的reads数目、碱基数目

 

001、

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

from Bio import SeqIO
import sys

fq1 = list(SeqIO.parse(sys.argv[1], "fastq"))
fq2 = list(SeqIO.parse(sys.argv[2], "fastq"))

total_reads = 0
total_bases = 0

for i in fq1:
        i = str(i.seq)
        total_reads += 1
        total_bases += len(i)
for i in fq2:
        i = str(i.seq)
        total_reads += 1
        total_bases += len(i)

print("total_reads: " + str(total_reads))
print("total_bases: " + str(total_bases))
(base) [b20223040323@admin1 test]$ python test.py SRR1770413_1.fastq SRR1770413_2.fastq
total_reads: 6
total_bases: 1806

 

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