comparison smart_toolShed/SMART/Java/Python/cleaning/CleanerChooser.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import sys
31 from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
32 from SMART.Java.Python.cleaning.GffCleaner import GffCleaner
33 from SMART.Java.Python.cleaning.GtfCleaner import GtfCleaner
34 from SMART.Java.Python.cleaning.DefaultCleaner import DefaultCleaner
35
36 #Attention!! Do not delete the imports!! They are used to know the type of file format!!!
37
38 class CleanerChooser(object):
39 """
40 A class that finds the correct cleaner
41 @ivar format: the format
42 @type format: string
43 @ivar cleaner: the parser
44 @type cleaner: object
45 @ivar cleanerClass: the class of the parser
46 @type cleanerClass: class
47 @ivar verbosity: verbosity
48 @type verbosity: int
49 """
50
51 def __init__(self, verbosity = 0):
52 """
53 Constructor
54 @param verbosity: verbosity
55 @type verbosity: int
56 """
57 self.verbosity = verbosity
58
59
60 def findFormat(self, format):
61 """
62 Find the correct parser
63 @ivar format: the format
64 @type format: string
65 @return: a cleaner
66 """
67 for cleanerClass in TranscriptListCleaner.__subclasses__():
68 if cleanerClass != None:
69 if cleanerClass.getFileFormats() != None and format in cleanerClass.getFileFormats():
70 self.cleanerClass = cleanerClass
71 return
72 self.cleanerClass = DefaultCleaner
73
74
75 def getCleaner(self):
76 """
77 Get the parser previously found
78 @return: the parser
79 """
80 return self.cleanerClass(self.verbosity)