Mercurial > repos > urgi-team > teiso

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author urgi-team
date Wed, 20 Jul 2016 05:00:24 -0400
parents
children
comparison
equal deleted inserted replaced
5:4093a2fb58be 6:20ec0d14798e
1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32 import os
33 from commons.core.checker.CheckerUtils import CheckerUtils
34 from commons.core.utils.RepetOptionParser import RepetOptionParser
35 from commons.core.utils.FileUtils import FileUtils
36 import subprocess
37
38 class Bowtie_build(object):
39
40 def __init__(self, input_reference = "", output_prefix= "", workingDir = "", verbosity = 3):
41
42 self._inputRef = input_reference
43 self._outPrefix = output_prefix
44 self._outputDir = workingDir
45 self._verbosity = verbosity
46
47 def setAttributesFromCmdLine(self):
48 description = "Create index for refrence file with bowtie-build.\n"
49 usage = "Bowtie_build -i <reference_in> -o <ebwt_outfile_base>\n"
50 print usage
51 parser = RepetOptionParser(description = description, usage = usage)
52 parser.add_option( '-i', '--input_reference', dest='input_reference', help='comma-separated list of files with ref sequences' )
53 parser.add_option( '-p', '--output_prefix', dest='output_prefix', help=' write Ebwt data to files with this dir/basename' )
54 parser.add_option( '-o', '--outputDir', dest='outputDir', help='result directory name', default = "")
55 options, args = parser.parse_args()
56 self.setAttributesFromOptions(options)
57
58 def setAttributesFromOptions(self, options):
59 self._inputRef = options.input_reference
60 self._outPrefix = options.output_prefix
61 self._outputDir = options.outputDir
62
63 def checkExecutables(self):
64 if not CheckerUtils.isExecutableInUserPath("bowtie2-build"):
65 raise Exception("ERROR: bowtie2-build must be in your path")
66
67 def checkOptions(self):
68 if self._inputRef != "":
69 if not FileUtils.isRessourceExists(self._inputRef):
70 raise Exception("ERROR: reference file %s does not exist!" % self._inputRef)
71 else:
72 raise Exception("ERROR: No specified -i option!")
73
74 if self._outPrefix == "":
75 raise Exception("ERROR: No specified -o option!")
76
77
78 def getBowtie2buildCmd(self, inputRef, outPrefix ):
79 cmd = 'bowtie2-build %s %s' % (inputRef, self._outPrefix )
80 #print cmd
81 return cmd
82
83 def run(self):
84
85 self.checkExecutables()
86 self.checkOptions()
87 try:
88 workingDir = self._outputDir
89 if os.path.exists(workingDir):
90 raise Exception("ERROR: %s already exists." % workingDir)
91 os.mkdir(workingDir)
92 os.chdir(workingDir)
93 os.symlink("%s" % self._inputRef,"%s.fa" % self._outPrefix)
94 cmd_bowtie = self.getBowtie2buildCmd(self._inputRef, self._outPrefix)
95 ## hide output of subprocess: stdout = index_dir_stderr
96 fstdout = open( "bowtie2_build.log" , 'w' )
97 process = subprocess.Popen(cmd_bowtie, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
98 returncode = process.wait()
99 fstdout.close()
100 # get stderr, allowing for case where it's very large
101 fstdout = open("bowtie2_build.log", 'rb' )
102 stderr = ''
103 buffsize = 1048576
104 try:
105 while True:
106 stderr += fstdout.read( buffsize )
107 if not stderr or len( stderr ) % buffsize != 0:
108 break
109 except OverflowError:
110 pass
111 fstdout.close()
112 if returncode != 0:
113 raise Exception, stderr
114 except Exception:
115 raise Exception("ERROR in %s " % cmd_bowtie)
116
117
118 if __name__ == "__main__":
119 print "heloo"
120 iLaunch = Bowtie_build()
121 iLaunch.setAttributesFromCmdLine()
122 iLaunch.run()
123