basic question???????? - Printable Version +- Python Forum (https://python-forum.io) +-- Forum: Python Coding (https://python-forum.io/forum-7.html) +--- Forum: General Coding Help (https://python-forum.io/forum-8.html) +--- Thread: basic question???????? (/thread-15452.html) |
basic question???????? - cemdede - Jan-17-2019 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. %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 RE: basic question???????? - metulburr - Jan-18-2019 what does not work? https://python-forum.io/misc.php?action=help&hid=19 RE: basic question???????? - ntd9395 - Jan-18-2019 (Jan-18-2019, 12:05 AM)metulburr Wrote: what does not work?out of range, ur index from 0 to 2 |