diff commons/launcher/LaunchRepeatMasker.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/LaunchRepeatMasker.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,113 @@
+#! /usr/bin/env python
+
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+import subprocess
+  
+class LaunchRepeatMasker(object):
+
+    def __init__(self,queryFileName="", libFileName ="",sensitivity="", engine="wu", cutOff=225, outputDir = ".",verbosity=0):
+        self._queryFileName = queryFileName
+        self._libFileName = libFileName
+        self._engine = engine
+        self._sensitivity = sensitivity
+        self._cutOff = cutOff
+        self._outputDir = outputDir
+        self._verbosity = verbosity
+         
+    def setAttributesFromCmdLine(self):
+        description = "LaunchRepeatMasker runs the RepeatMasker program  ."    
+        parser = RepetOptionParser(description = description)
+        parser.add_option("-q", "--query", dest="queryFileName", default = None,  action="store", type="string", help="input query file [compulsory] [format: fasta]")
+        parser.add_option("-l", "--libFileName", dest="libFileName", default = None,  action="store", type="string", help="custom library [optional]")  
+        parser.add_option("-n", "--outputDir", dest="outputDir", default=".", action="store", type="string", help="outputDir (default : current directory) [optional] ")  
+        parser.add_option("-c", "--cutOff", dest="cutOff", default=225, action="store", type="int", help="Sets cutoff score for masking repeats when using -lib (default 225) [optional] ")
+        parser.add_option("-e", "--engine", dest="engine", default = "wu",  action="store", type="string", help="engine  [optional] ")    
+        parser.add_option("-u", "--sensitivity", dest="sensitivity", default = "",  action="store", type="string", help="sensitivity  can be s, q, qq[optional] ")    
+        parser.add_option("-v", "--verbosity", dest="verbosity", default = 0,  action="store", type="int", help="verbosity [optional] ")    
+
+        (options, args) = parser.parse_args()
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._queryFileName = options.queryFileName
+        self._libFileName = options.libFileName
+        self._outputDir = options.outputDir
+        self._engine = options.engine
+        self._sensitivity = options.sensitivity
+        self._cutOff = options.cutOff
+        self._verbosity = options.verbosity
+        
+    def checkOptions(self):       
+        if self._queryFileName != "":
+            if not FileUtils.isRessourceExists(self._queryFileName):
+                raise Exception("ERROR: Query file: %s does not exist!" % self._queryFileName)
+        else:
+            raise Exception("ERROR: No specified --query option!")
+                                
+    def run(self):
+        if not CheckerUtils.isExecutableInUserPath("RepeatMasker") :
+            print "ERROR: RepeatMasker must be in your path"
+        else:
+            self.checkOptions()
+            
+            engine = ""
+            if self._engine == "wu":
+                engine = "-e wublast"
+            elif self._engine == "cm":
+                engine = "-e crossmatch"
+            sensitivity = ""
+            if self._sensitivity:
+                sensitivity = "-%s" % self._sensitivity     
+            libFileName = ""
+            if self._libFileName != "":
+                libFileName = "-lib %s" % self._libFileName
+
+            cmd = "RepeatMasker %s -dir %s -pa 1 -gccalc -no_is -nolow %s %s %s" % (self._queryFileName,self._outputDir,engine,sensitivity,libFileName)
+            cmd = cmd.split() 
+            
+            if self._verbosity>0:
+                print("Running RepeatMasker with following commands : %s" %cmd)
+            
+            process = subprocess.Popen(cmd, stdout=subprocess.PIPE,stderr = subprocess.PIPE)
+#            process.wait()
+            output= process.communicate()
+            if self._verbosity>0:
+                print("".join(output))
+            return process.returncode
+            
+if __name__ == "__main__":
+    iLaunchRepeatMasker = LaunchRepeatMasker()
+    iLaunchRepeatMasker.setAttributesFromCmdLine()
+    iLaunchRepeatMasker.run()
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