diff qcma-55561a945415/HumMeth27QCReport/HumMeth27QCReport.py @ 0:8933ecfb6ab2 default tip

Uploaded

--- /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 ([e-mail])
+#
+# 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