python

照方抓药

import time
start = time.time()
import glob
import gzip
length=[]
with gzip.open('H-CK-1-3_clean.fq.gz','rt') as fp:
    i = 0 
    for line in fp:
        i += 1
        if i % 4 == 2: 
            if len(line)-1==50:
                length.append(i-1)
                length.append(i)
                length.append(i+1)
                length.append(i+2)
f = gzip.open('H-CK-1-3_clean.fq.gz','rt')
length.append('0')
output_fastq = open("temp2.fq",'w')
i = 0
N = 0
for line in f:
    N += 1
    if N == length[i]:
        output_fastq.write(line)
        i += 1
output_fastq.close()
end = time.time()
print("used %s s" % str(end - start))

2

import time
start = time.time()
import glob
import gzip
fp = gzip.open('test.fq.gz','rt')
fastq = open("temp5.fq",'w')
i = 0 
for line in fp:
    i += 1
    if i%4 ==1: 
        line1=line
    elif i%4 ==2: 
        line2=line
    elif i%4 ==3: 
        line3=line
    elif i%4 ==0: 
        line4=line
        if len(line4)-1==50:
            fastq.write(line1+line2+line3+line4)
fastq.close()
end = time.time()
print("used %s s" % str(end - start))