Mercurial > repos > yufei-luo > s_mart
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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| -1:000000000000 | 0:e0f8dcca02ed |
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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) |