Mercurial > repos > stemcellcommons > spp_tool

comparison spp_wrapper.py @ 8:2db63ab9b129

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Uploaded
author modencode-dcc
date Fri, 18 Jan 2013 19:01:39 -0500
parents cbbc26d6ca30
children dfdaa943f855
comparison
equal deleted inserted replaced
7:cbbc26d6ca30 8:2db63ab9b129
34 cmdline = "%s -i=%s" % ( cmdline, input_file ) 34 cmdline = "%s -i=%s" % ( cmdline, input_file )
35 35
36 #set additional options 36 #set additional options
37 #======================================================================================== 37 #========================================================================================
38 if (options['action'] == "cross_correlation"): 38 if (options['action'] == "cross_correlation"):
39 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'] )
40 elif (options['action'] == "peak_calling"): 40 elif (options['action'] == "peak_calling"):
41 cmdline = "%s -fdr=%s -npeak=%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['fdr'], options['npeak'], options['savr'], options['savd'], options['savn'], options['savp'], options['rf'] ) 41 cmdline = "%s -fdr=%s -npeak=%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['fdr'], options['npeak'], options['savr'], options['savd'], options['savn'], options['savp'], options['rf'] )
42 elif (options['action'] == "idr"): 42 elif (options['action'] == "idr"):
43 cmdline = "%s -npeak=%s %s %s %s %s > default_output.txt" % ( cmdline, options['npeak'], options['savr'], options['savp'], options['out'], options['rf'] ) 43 cmdline = "%s -npeak=%s %s %s %s %s > default_output.txt" % ( cmdline, options['npeak'], options['savr'], options['savp'], options['out'], options['rf'] )
44 elif (options['action'] == "custom"): 44 elif (options['action'] == "custom"):
45 cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] ) 45 cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] )
46 cmdline = "%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] ) 46 cmdline = "%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] )
47 47
48 #run cmdline 48 #run cmdline
49 #======================================================================================== 49 #========================================================================================
50 tmp_dir = tempfile.mkdtemp() 50 tmp_dir = tempfile.mkdtemp()
51 stderr_name = tempfile.NamedTemporaryFile().name 51 stderr_name = tempfile.NamedTemporaryFile().name