Mercurial > repos > bornea > dotplot_runner

comparison dotplot_runner.py @ 4:a0b4bcf67972 draft

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Uploaded
author bornea
date Fri, 29 Jan 2016 10:00:21 -0500
parents 7e98f893e9ae
children
comparison
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3:fcc56a8fc3a0 4:a0b4bcf67972
24 24
25 import os 25 import os
26 import sys 26 import sys
27 27
28 28
29 FDR1 = sys.argv[2]
30 FDR2 = sys.argv[3]
31 spec_max = sys.argv[4]
32 os.rename(sys.argv[1], "saint_input.txt")
33 ins_path = sys.argv[9]
34
35
29 dirs_list = [] 36 dirs_list = []
30 for (dirpath, dirnames, filename) in os.walk(str(ins_path)): 37 for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
31 dirs_list.extend(dirnames) 38 dirs_list.extend(dirnames)
32 break 39 break
33 if r"Dotplot_Release" in dirs_list: 40 if r"Dotplot_Release" in dirs_list:
34 pass 41 pass
35 else: 42 else:
36 cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz" 43 cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz"
37 os.system(cmd) 44 os.system(cmd)
38 45
39
40 FDR1 = sys.argv[2]
41 FDR2 = sys.argv[3]
42 spec_max = sys.argv[4]
43 os.rename(sys.argv[1], "saint_input.txt")
44 ins_path = sys.argv[9]
45 46
46 cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) + 47 cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) +
47 r" -t " + str(FDR2) + " -m " + str(spec_max)) 48 r" -t " + str(FDR2) + " -m " + str(spec_max))
48 os.system(cmd) 49 os.system(cmd)
49 50