diff TEisotools-1.1.a/TEiso/Bowtie_build.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/TEiso/Bowtie_build.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-#!/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()
-