Jan-17-2019, 09:39 PM
Hi everyone, I just could not figure out why this one does not work under jupyter notebook.
I tried to take the *.sam files, use the tool on the files and put the output bam file into bam folder.
I tried to take the *.sam files, use the tool on the files and put the output bam file into bam folder.
%pylab inline import glob import os as os import pandas as pd import numpy as np
if not os.path.exists('./bam'):
os.makedirs('./bam')
filelist=glob.glob('./sam/*.sam')
for i in filelist:
sample=i.split('/')
sample=sample[2]
sample_s=sample.split('.')
file_in='view -S -b ./sam/%s > \
./bam/%s.bam' %(sample,i,sample_s[0])
! samtools $file_in