Mercurial > repos > yufei-luo > s_mart
comparison commons/launcher/LaunchRepeatMasker.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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() |