diff TEisotools-1.0/TEiso/Bowtie_build.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/TEiso/Bowtie_build.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,123 @@
+#!/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.
+import os
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+from commons.core.utils.FileUtils import FileUtils
+import subprocess
+
+class Bowtie_build(object):
+         
+    def __init__(self, input_reference = "", output_prefix= "", workingDir = "", verbosity = 3):
+       
+        self._inputRef = input_reference
+        self._outPrefix = output_prefix
+        self._outputDir = workingDir
+        self._verbosity = verbosity
+        
+    def setAttributesFromCmdLine(self):
+        description = "Create index for refrence file with bowtie-build.\n" 
+        usage = "Bowtie_build -i <reference_in> -o <ebwt_outfile_base>\n"
+        print usage
+        parser = RepetOptionParser(description = description, usage = usage)
+        parser.add_option( '-i', '--input_reference', dest='input_reference', help='comma-separated list of files with ref sequences' )
+        parser.add_option( '-p', '--output_prefix', dest='output_prefix', help=' write Ebwt data to files with this dir/basename' )
+        parser.add_option( '-o', '--outputDir', dest='outputDir', help='result directory name', default = "")
+        options, args = parser.parse_args()
+        self.setAttributesFromOptions(options)
+    
+    def setAttributesFromOptions(self, options):
+        self._inputRef = options.input_reference
+        self._outPrefix = options.output_prefix
+        self._outputDir = options.outputDir
+        
+    def checkExecutables(self):
+        if not CheckerUtils.isExecutableInUserPath("bowtie2-build"):
+            raise Exception("ERROR: bowtie2-build must be in your path")
+    
+    def checkOptions(self):   
+        if self._inputRef != "":
+            if not FileUtils.isRessourceExists(self._inputRef):
+                raise Exception("ERROR: reference file %s does not exist!" % self._inputRef)
+        else:
+            raise Exception("ERROR: No specified -i option!")
+        
+        if self._outPrefix == "":
+            raise Exception("ERROR: No specified -o option!")
+    
+   
+    def getBowtie2buildCmd(self, inputRef, outPrefix ): 
+        cmd = 'bowtie2-build %s %s' % (inputRef, self._outPrefix )
+        #print cmd
+        return cmd
+    
+    def run(self):
+        
+        self.checkExecutables()
+        self.checkOptions()
+        try:
+            workingDir = self._outputDir
+            if os.path.exists(workingDir):
+                raise Exception("ERROR: %s already exists." % workingDir)
+            os.mkdir(workingDir)
+            os.chdir(workingDir)
+            os.symlink("%s" % self._inputRef,"%s.fa" % self._outPrefix)
+            cmd_bowtie = self.getBowtie2buildCmd(self._inputRef, self._outPrefix)
+            ## hide output of subprocess: stdout = index_dir_stderr
+            fstdout = open( "bowtie2_build.log" , 'w' )
+            process = subprocess.Popen(cmd_bowtie, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
+            returncode = process.wait()
+            fstdout.close()
+            # get stderr, allowing for case where it's very large
+            fstdout = open("bowtie2_build.log", 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += fstdout.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                    pass
+            fstdout.close()
+            if returncode != 0:
+                    raise Exception, stderr
+        except Exception:
+            raise Exception("ERROR in %s " % cmd_bowtie)
+        
+                
+if __name__ == "__main__":
+    print "heloo"
+    iLaunch = Bowtie_build()
+    iLaunch.setAttributesFromCmdLine()
+    iLaunch.run()
+