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