/usr/share/giira/scripts/sortReaSam.py is in giira 0.0.20140625-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | # -*- coding: utf-8 -*-
"""
Copyright (c) 2013,
Franziska Zickmann,
ZickmannF@rki.de, Robert Koch-Institute, Berlin, Germany
Distributed under the GNU Lesser General Public License, version 3.0
"""
#!/usr/bin/env python
import os
import sys
pathOut = sys.argv[1]
syscall1 = "samtools view -b -S %sresultsRun/reassignedReads.sam > %sresultsRun/reassignedReads.bam" %(pathOut,pathOut)
print syscall1
os.system(syscall1)
syscall2 = "samtools sort -n %sresultsRun/reassignedReads.bam %sresultsRun/reassignedReads_sorted" %(pathOut,pathOut)
print syscall2
os.system(syscall2)
syscall3 = "samtools view -h -o %sresultsRun/reassignedReads_sorted.sam %sresultsRun/reassignedReads_sorted.bam" %(pathOut,pathOut)
print syscall3
os.system(syscall3)
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