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comparison HumMeth27QCReport/HumMeth27QCReport.py @ 0:55561a945415 default tip

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Migrated tool version 1.0 from old tool shed archive to new tool shed repository
author andreu
date Tue, 07 Jun 2011 17:26:58 -0400
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-1:000000000000 0:55561a945415
1 # Based on rgQC.py by ross lazarus (Version from 20100914)
2
3 ########################################################################
4 # HumMeth27QCReport.py a parser of the HumMeth27QCReport R package
5 # Copyright (C) 2011 Andreu Alibes (aalibes@gmail.com)
6 #
7 # This program is free software: you can redistribute it and/or modify
8 # it under the terms of the GNU General Public License as published by
9 # the Free Software Foundation, either version 3 of the License, or
10 # (at your option) any later version.
11 #
12 # This program is distributed in the hope that it will be useful,
13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 # GNU General Public License for more details.
16 #
17 # You should have received a copy of the GNU General Public License
18 # along with this program. If not, see <http://www.gnu.org/licenses/>.
19 ########################################################################
20 from optparse import OptionParser
21 import os, sys
22
23 if __name__ == "__main__":
24 u = """ called in xml as
25 <command interpreter="python">
26 HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX'
27 -1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path'
28 </command>
29
30 """
31 progname = os.path.basename(sys.argv[0])
32 if len(sys.argv) < 14:
33 print '%s requires at least 14 parameters - got %d = %s' % (progname,len(sys.argv),sys.argv)
34 sys.exit(1)
35 parser = OptionParser(usage=u, version="%prog 0.01")
36 a = parser.add_option
37 a("-a","--avefile",dest="avefile")
38 a("-c","--ctrfile",dest="ctrfile")
39 a("-s","--smplfile",dest="smplfile")
40 a("-d","--discfile",dest="discfile")
41 a("-l","--platf",dest="platf")
42 a("-v","--pval",dest="pval")
43 a("-m","--clustmethd",dest="clustmethd")
44 a("-x","--chrx",dest="chrx")
45 a("-1","--oQualityCheck",dest="oQualityCheck")
46 a("-2","--oSample",dest="oSample")
47 a("-3","--oInternalControl",dest="oInternalControl")
48 a("-4","--oExplorativeAnalysis",dest="oExplorativeAnalysis")
49 a("-5","--oNormalizedMvalues",dest="oNormalizedMvalues")
50 a("-6","--oQC_Analysis",dest="oQC_Analysis")
51 a("-p","--patho",dest="newfpath")
52
53 (options,args) = parser.parse_args()
54 avefile = options.avefile
55 ctrfile = options.ctrfile
56 smplfile = options.smplfile
57 discfile = options.discfile
58 platf = options.platf
59 pval = options.pval
60 clustmethd = options.clustmethd
61 chrx = options.chrx
62 oQualityCheck = options.oQualityCheck
63 oSample = options.oSample
64 oInternalControl = options.oInternalControl
65 oExplorativeAnalysis = options.oExplorativeAnalysis
66 oNormalizedMvalues = options.oNormalizedMvalues
67 oQC_Analysis = options.oQC_Analysis
68
69 newfpath = options.newfpath
70 newfpath = os.path.realpath(newfpath)
71 try:
72 os.makedirs(newfpath)
73 except:
74 pass
75 try:
76 os.system("cp " + avefile + " " + newfpath+"/AvgBeta.txt")
77 os.system("cp " + ctrfile + " " + newfpath+"/Control.txt")
78 os.system("cp " + smplfile + " " + newfpath+"/Sample.txt")
79 if(discfile != 'None'):
80 os.system("cp " + discfile + " " + newfpath+"/Discard.txt")
81
82 execstring = "/data/apache/galaxy.test.crg/htdocs/galaxy-dist/tools/CRG-Tools/HumMeth27QCReport.R \"Directory=\'"+newfpath+"\'\" \"Plat=\'"+platf+"\'\" \"pvalue=\'"+pval+"\'\" \"chrom=\'"+chrx+"\'\" \"method=\'"+clustmethd+"\'\""
83 os.system(execstring + " 2> /dev/null")
84 os.system("cd " + newfpath + "; mv Sample.pdf " + oSample + "; mv InternalControl.pdf " + oInternalControl + ";mv QualityCheck.pdf " + oQualityCheck + ";mv ExplorativeAnalysis.pdf " + oExplorativeAnalysis + ";mv NormalizedMvalues.txt " + oNormalizedMvalues + ";mv QC_Analysis.xls " + oQC_Analysis )
85 except:
86 pass