Mercurial > repos > jiechenable1987 > qqq_test
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.py Fri Feb 24 17:42:16 2012 -0500 @@ -0,0 +1,86 @@ +# Based on rgQC.py by ross lazarus (Version from 20100914) + +######################################################################## +# HumMeth27QCReport.py a parser of the HumMeth27QCReport R package +# Copyright (C) 2011 Andreu Alibes (aalibes@gmail.com) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +######################################################################## +from optparse import OptionParser +import os, sys + +if __name__ == "__main__": + u = """ called in xml as + <command interpreter="python"> + HumMeth27QCReport.py -a '$inputAVE' -c '$inputCTRL' -s '$inputSAMPLE' -d '$inputDISC' -l '$platform' -v '$pval' -m '$ClustMethod' -x '$ChrX' +-1 '$oQualityCheck' -2 '$oSample' -3 '$oInternalControl' -4 '$oExplorativeAnalysis' -5 '$oNormalizedMvalues' -6 '$oQC_Analysis' -p '$oQualityCheck.files_path' + </command> + + """ + progname = os.path.basename(sys.argv[0]) + if len(sys.argv) < 14: + print '%s requires at least 14 parameters - got %d = %s' % (progname,len(sys.argv),sys.argv) + sys.exit(1) + parser = OptionParser(usage=u, version="%prog 0.01") + a = parser.add_option + a("-a","--avefile",dest="avefile") + a("-c","--ctrfile",dest="ctrfile") + a("-s","--smplfile",dest="smplfile") + a("-d","--discfile",dest="discfile") + a("-l","--platf",dest="platf") + a("-v","--pval",dest="pval") + a("-m","--clustmethd",dest="clustmethd") + a("-x","--chrx",dest="chrx") + a("-1","--oQualityCheck",dest="oQualityCheck") + a("-2","--oSample",dest="oSample") + a("-3","--oInternalControl",dest="oInternalControl") + a("-4","--oExplorativeAnalysis",dest="oExplorativeAnalysis") + a("-5","--oNormalizedMvalues",dest="oNormalizedMvalues") + a("-6","--oQC_Analysis",dest="oQC_Analysis") + a("-p","--patho",dest="newfpath") + + (options,args) = parser.parse_args() + avefile = options.avefile + ctrfile = options.ctrfile + smplfile = options.smplfile + discfile = options.discfile + platf = options.platf + pval = options.pval + clustmethd = options.clustmethd + chrx = options.chrx + oQualityCheck = options.oQualityCheck + oSample = options.oSample + oInternalControl = options.oInternalControl + oExplorativeAnalysis = options.oExplorativeAnalysis + oNormalizedMvalues = options.oNormalizedMvalues + oQC_Analysis = options.oQC_Analysis + + newfpath = options.newfpath + newfpath = os.path.realpath(newfpath) + try: + os.makedirs(newfpath) + except: + pass + try: + os.system("cp " + avefile + " " + newfpath+"/AvgBeta.txt") + os.system("cp " + ctrfile + " " + newfpath+"/Control.txt") + os.system("cp " + smplfile + " " + newfpath+"/Sample.txt") + if(discfile != 'None'): + os.system("cp " + discfile + " " + newfpath+"/Discard.txt") + + execstring = "/data/apache/galaxy.test.crg/htdocs/galaxy-dist/tools/CRG-Tools/HumMeth27QCReport.R \"Directory=\'"+newfpath+"\'\" \"Plat=\'"+platf+"\'\" \"pvalue=\'"+pval+"\'\" \"chrom=\'"+chrx+"\'\" \"method=\'"+clustmethd+"\'\"" + os.system(execstring + " 2> /dev/null") + 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 ) + except: + pass