Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/cleaning/CleanerChooser.py @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
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30 import sys
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31 from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
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32 from SMART.Java.Python.cleaning.GffCleaner import GffCleaner
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33 from SMART.Java.Python.cleaning.GtfCleaner import GtfCleaner
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34 from SMART.Java.Python.cleaning.DefaultCleaner import DefaultCleaner
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35
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36 #Attention!! Do not delete the imports!! They are used to know the type of file format!!!
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37
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38 class CleanerChooser(object):
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39 """
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40 A class that finds the correct cleaner
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41 @ivar format: the format
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42 @type format: string
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43 @ivar cleaner: the parser
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44 @type cleaner: object
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45 @ivar cleanerClass: the class of the parser
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46 @type cleanerClass: class
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 @ivar verbosity: verbosity
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48 @type verbosity: int
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49 """
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50
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51 def __init__(self, verbosity = 0):
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52 """
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53 Constructor
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54 @param verbosity: verbosity
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55 @type verbosity: int
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56 """
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57 self.verbosity = verbosity
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58
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59
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60 def findFormat(self, format):
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61 """
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62 Find the correct parser
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63 @ivar format: the format
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64 @type format: string
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65 @return: a cleaner
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66 """
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67 for cleanerClass in TranscriptListCleaner.__subclasses__():
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68 if cleanerClass != None:
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69 if cleanerClass.getFileFormats() != None and format in cleanerClass.getFileFormats():
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70 self.cleanerClass = cleanerClass
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71 return
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72 self.cleanerClass = DefaultCleaner
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73
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74
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75 def getCleaner(self):
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76 """
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77 Get the parser previously found
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78 @return: the parser
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79 """
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80 return self.cleanerClass(self.verbosity)