Mercurial > repos > jiechenable1987 > qqq_test
comparison qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.py @ 0:8933ecfb6ab2 default tip
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author | jiechenable1987 |
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date | Fri, 24 Feb 2012 17:42:16 -0500 |
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-1:000000000000 | 0:8933ecfb6ab2 |
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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 |