生信脚本练习（7）求fastq文件质量值分布

这里是求fastq文件的质量类型和比例
注意数几种类型用了set() 的方法

with open("Test1.fastq","r") as f:
    lines = f.readlines()
qual = []
for line in lines:
    if lines.index(line)% 4 == 3:
        line= line.strip('\n')
        qual.append(line)
qual = "".join(qual)
unique = list(set(qual))
number = []
for u in unique:
    for q in qual:
        number.append(qual.count(u))
number = list(set(number))
with open("1-2.txt","w") as f:
    f.write("QUAL"+"\t" + "TOTAL"+ '\n')
    for i in range(len(number)):
        f.write(str(unique[i])+"\t"+str(number[i])+"\n")

然后画个饼图

data <- read.table("c:\\Users\\1-2.txt")
#print(data)
jpeg("c:\\Users\\pie.jpeg",width=2000,height=2000,res=300)
pct <- round(val/sum(val)*100)
lbls2 <- paste(key, "  ", pct,"%",sep = "")
pie(val,labels = lbls2,main = "Pie Chart of Qual")#,col = rainbow(length(lbls2)))
dev.off()

8.14更新更好的解法：
就是用字典嘛

from collections import Counter
with open("c:/Test1.fastq","r") as f:
    count = 0
    qual = {}
    while True:
        line = f.readline().strip()
        count += 1
        if count % 4 == 0:
            q = ((Counter(line)))
            for k,v in q.items():
                if k not in qual:
                    qual[k] = 0
                else:
                    qual[k] += v
        if len(line) == 0:
            break
print(qual)
with open("c:/1-2.txt","w") as f:
    f.write("QUAL"+"\t" + "TOTAL"+ '\n')
    for k,v in qual.items():
        f.write(k + '\t'+ str(v) + '\n')