Mercurial > repos > zzhou > spp_phantompeak

comparison spp_wrapper.py @ 19:663ef5410dd7 draft default tip

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author zzhou
date Thu, 29 Nov 2012 13:50:59 -0500
parents 5648b4efe736
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18:16ae2b869253 19:663ef5410dd7
18 output_rdata_file = sys.argv[5] 18 output_rdata_file = sys.argv[5]
19 output_plot_file = sys.argv[6] 19 output_plot_file = sys.argv[6]
20 output_default_file = sys.argv[7] 20 output_default_file = sys.argv[7]
21 script_path = sys.argv[8] 21 script_path = sys.argv[8]
22 22
23 cmd = "tar -czvf spp_1.10.1.tar spp"
24 os.system(cmd)
25 cmd = "gzip spp_1.10.1.tar"
26 os.system(cmd)
27 cmd = "Rscript %s/deploy_spp.R" % script_path
28 os.system(cmd)
29
30 #set file extensions and set mandatory options 23 #set file extensions and set mandatory options
31 #======================================================================================== 24 #========================================================================================
32 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name 25 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name
33 26
34 chip_file = "%s.bam" % (options['chip_file']) 27 chip_file = "%s.bam" % (options['chip_file'])
38 if 'input_file' in options: 31 if 'input_file' in options:
39 input_file = "%s.bam" % (options['input_file']) 32 input_file = "%s.bam" % (options['input_file'])
40 subprocess.call(["cp", options['input_file'], input_file]) 33 subprocess.call(["cp", options['input_file'], input_file])
41 cmdline = "%s -i=%s" % ( cmdline, input_file ) 34 cmdline = "%s -i=%s" % ( cmdline, input_file )
42 35
43 #test = "%s_VS_%s.narrowPeak.gz" %(chip_name, input_name)
44 #print test
45 #set additional options 36 #set additional options
46 #======================================================================================== 37 #========================================================================================
47 if (options['action'] == "cross_correlation"): 38 if (options['action'] == "cross_correlation"):
48 cmdline = "%s %s %s %s > default_output.txt" % ( cmdline, options['savp'], options['out'], options['rf'] ) 39 cmdline = "%s %s %s %s > default_output.txt" % ( cmdline, options['savp'], options['out'], options['rf'] )
49 elif (options['action'] == "peak_calling"): 40 elif (options['action'] == "peak_calling"):