view commons/core/parsing/ @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -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
# "".
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
import re
import sys
	 import cPickle as pickle
	 import pickle
from SMART.Java.Python.structure.Interval import Interval
from commons.core.parsing.TranscriptListParser import TranscriptListParser
from SMART.Java.Python.structure.Transcript import Transcript

class PklParser(TranscriptListParser):
	"""A class that parses the intern PKL file and create a transcript list"""
	def __init__(self, fileName, verbosity = 1):
		self.title = None
		super(PklParser, self).__init__(fileName, verbosity)
		self.handle		   = open(fileName, "rb")
		self.verbosity	   = verbosity
		self.initAddress   = 0
		self.address	   = self.initAddress
		self.over		   = False
		self.chromosome	= None

	def __del__(self):
		super(PklParser, self).__del__()

	def getFileFormats():
		return ["pkl"]
	getFileFormats = staticmethod(getFileFormats)

	def skipFirstLines(self):

	def reset(self):
		self.initAddress = 0

	def setChromosome(self, chromosome):
		self.chromosome = chromosome

	def gotoAddress(self, address):
		self.address = address

	def getNextTranscript(self):
		self.address = self.handle.tell()
			transcript = pickle.load(self.handle)
			if self.chromosome != None and transcript.getChromosome() != self.chromosome:
				self.over = True
				return False
			return transcript
		except EOFError:
			self.over = True
			return False

	def getIterator(self):
		while True:
			transcript = self.getNextTranscript()
			if not transcript:
				self.over = True
			yield transcript

	def setInitAddress(self, address):
		self.initAddress = address

	def getCurrentTranscriptAddress(self):
		return self.address

	def isOver(self):
		return self.over