Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
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
33 from commons.core.checker.CheckerUtils import CheckerUtils
34 from commons.core.utils.FileUtils import FileUtils
35 from commons.core.utils.RepetOptionParser import RepetOptionParser
36 import subprocess
37
38 class LaunchRepeatMasker(object):
39
40 def __init__(self,queryFileName="", libFileName ="",sensitivity="", engine="wu", cutOff=225, outputDir = ".",verbosity=0):
41 self._queryFileName = queryFileName
42 self._libFileName = libFileName
43 self._engine = engine
44 self._sensitivity = sensitivity
45 self._cutOff = cutOff
46 self._outputDir = outputDir
47 self._verbosity = verbosity
48
49 def setAttributesFromCmdLine(self):
50 description = "LaunchRepeatMasker runs the RepeatMasker program ."
51 parser = RepetOptionParser(description = description)
52 parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]")
53 parser.add_option("-l", "--libFileName", dest="libFileName", default = None, action="store", type="string", help="custom library [optional]")
54 parser.add_option("-n", "--outputDir", dest="outputDir", default=".", action="store", type="string", help="outputDir (default : current directory) [optional] ")
55 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] ")
56 parser.add_option("-e", "--engine", dest="engine", default = "wu", action="store", type="string", help="engine [optional] ")
57 parser.add_option("-u", "--sensitivity", dest="sensitivity", default = "", action="store", type="string", help="sensitivity can be s, q, qq[optional] ")
58 parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ")
59
60 (options, args) = parser.parse_args()
61 self._setAttributesFromOptions(options)
62
63 def _setAttributesFromOptions(self, options):
64 self._queryFileName = options.queryFileName
65 self._libFileName = options.libFileName
66 self._outputDir = options.outputDir
67 self._engine = options.engine
68 self._sensitivity = options.sensitivity
69 self._cutOff = options.cutOff
70 self._verbosity = options.verbosity
71
72 def checkOptions(self):
73 if self._queryFileName != "":
74 if not FileUtils.isRessourceExists(self._queryFileName):
75 raise Exception("ERROR: Query file: %s does not exist!" % self._queryFileName)
76 else:
77 raise Exception("ERROR: No specified --query option!")
78
79 def run(self):
80 if not CheckerUtils.isExecutableInUserPath("RepeatMasker") :
81 print "ERROR: RepeatMasker must be in your path"
82 else:
83 self.checkOptions()
84
85 engine = ""
86 if self._engine == "wu":
87 engine = "-e wublast"
88 elif self._engine == "cm":
89 engine = "-e crossmatch"
90 sensitivity = ""
91 if self._sensitivity:
92 sensitivity = "-%s" % self._sensitivity
93 libFileName = ""
94 if self._libFileName != "":
95 libFileName = "-lib %s" % self._libFileName
96
97 cmd = "RepeatMasker %s -dir %s -pa 1 -gccalc -no_is -nolow %s %s %s" % (self._queryFileName,self._outputDir,engine,sensitivity,libFileName)
98 cmd = cmd.split()
99
100 if self._verbosity>0:
101 print("Running RepeatMasker with following commands : %s" %cmd)
102
103 process = subprocess.Popen(cmd, stdout=subprocess.PIPE,stderr = subprocess.PIPE)
104 # process.wait()
105 output= process.communicate()
106 if self._verbosity>0:
107 print("".join(output))
108 return process.returncode
109
110 if __name__ == "__main__":
111 iLaunchRepeatMasker = LaunchRepeatMasker()
112 iLaunchRepeatMasker.setAttributesFromCmdLine()
113 iLaunchRepeatMasker.run()