view smart_toolShed/SMART/Java/Python/cleaning/ @ 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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# Copyright INRA-URGI 2009-2010
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "".
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# modify and redistribute granted by the license, users are provided only
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# The fact that you are presently reading this means that you have had
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import sys
from import TranscriptListCleaner
from import GffCleaner
from import GtfCleaner
from import DefaultCleaner

#Attention!! Do not delete the imports!! They are used to know the type of file format!!!

class CleanerChooser(object):
	A class that finds the correct cleaner
	@ivar format: the format
	@type format: string
	@ivar cleaner: the parser
	@type cleaner: object
	@ivar cleanerClass: the class of the parser
	@type cleanerClass: class
	@ivar verbosity: verbosity
	@type verbosity: int		

	def __init__(self, verbosity = 0):
		@param verbosity: verbosity
		@type verbosity: int
		self.verbosity = verbosity

	def findFormat(self, format):
		Find the correct parser
		@ivar format: the format
		@type format: string
		@return: a cleaner
		for cleanerClass in TranscriptListCleaner.__subclasses__():
			if cleanerClass != None:
				if cleanerClass.getFileFormats() != None and format in cleanerClass.getFileFormats():
					self.cleanerClass = cleanerClass
		self.cleanerClass = DefaultCleaner

	def getCleaner(self):
		Get the parser previously found
		@return: the parser
		return self.cleanerClass(self.verbosity)