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| import os | |
| commandList = [] | |
| ### Download data | |
| commandList.append("wget https://berkeley.box.com/shared/static/m3x4czbxbh87vq078li3llr3w0ba3i8n.tar -O dataset0.tar") | |
| commandList.append("tar -xvf dataset0.tar") | |
| commandList.append("wget https://berkeley.box.com/shared/static/pq98sgh3lb6vqvxrsczfrphidf1ik1gj.tar -O dataset1.tar") | |
| commandList.append("tar xvf dataset1.tar") | |
| commandList.append("wget https://berkeley.box.com/shared/static/h05c4hl6fk8h8k95w0y17jtkeuzsz0kp.tar -O dataset2.tar") | |
| commandList.append("tar xvf dataset2.tar") | |
| commandList.append("wget https://berkeley.box.com/shared/static/7ub5gqnd61pfvay6knl0ipklmrbzcsjq.tar -O dataset3.tar") | |
| commandList.append("tar xvf dataset3.tar") | |
| ### Install tools | |
| commandList.append("wget http://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download -O ./mummer.tar.gz") | |
| commandList.append("tar -zxvf ./mummer.tar.gz -C ./") | |
| commandList.append("make install -C ./MUMmer3.23/") | |
| commandList.append("wget https://sourceforge.net/projects/quast/files/quast-2.3.tar.gz/download -O quast-2.3.tar.gz") | |
| commandList.append("tar -zxvf quast-2.3.tar.gz ") | |
| ### Run tools | |
| for i in range(4): | |
| commandList.append("python -m srcRefactor.misassemblyFixerLib.mFixer dataset"+str(i) +"/ ./MUMmer3.23/") | |
| commandList.append("python -m srcRefactor.repeatPhaserLib.aSplitter dataset"+str(i) +"/ ./MUMmer3.23/") | |
| commandList.append("python ./quast-2.3/quast.py -R dataset"+str(i)+"/reference.fasta dataset"+str(i) +"/LC.fasta dataset"+str(i) +"/mFixed.fasta dataset"+str(i) +"/abun.fasta") | |
| ### Final print | |
| commandList.append("find . -name 'report.txt' | xargs cat > allinoneeport.txt ") | |
| for eachCommand in commandList : | |
| os.system(eachCommand) | |