diff commons/core/parsing/NCListParser.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/NCListParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,125 @@
+#
+# Copyright INRA-URGI 2009-2012
+# 
+# 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
+# "http://www.cecill.info".
+# 
+# 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
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.ncList.NCList import NCList
+from SMART.Java.Python.ncList.NCListCursor import NCListCursor
+from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+try:
+   import cPickle as pickle
+except:
+   import pickle
+
+
+class NCListParser(TranscriptListParser):
+
+
+	def __init__(self, fileName, verbosity = 0):
+		self.title = None
+		TranscriptListParser.__init__(self, fileName, verbosity)
+		self.parse()
+
+	def getFileFormats():
+		return ["nclist"]
+	getFileFormats = staticmethod(getFileFormats)
+
+	def skipFirstLines(self):
+		return
+
+	def parse(self):
+		handle                       = open(self.fileName)
+		self.sortedFileNames         = pickle.load(handle)
+		self.nbElements	             = pickle.load(handle)
+		self.nbElementsPerChromosome = pickle.load(handle)
+		self.ncLists                 = pickle.load(handle)
+		for ncList in self.ncLists.values():
+			ncList._reopenFiles()
+		handle.close()
+		self.chromosomes     = sorted(self.nbElementsPerChromosome.keys())
+		self.fileNames       = dict([chromosome, self.ncLists[chromosome]._transcriptFileName] for chromosome in self.chromosomes)
+		self.currentReader   = None
+		self.currentChrIndex = 0
+
+	def getSortedFileNames(self):
+		return self._sortedFileNames
+
+	def getNbElements(self):
+		return self._nbElements
+
+	def getNbElementsPerChromosome(self):
+		return self._nbElementsPerChromosome
+
+	def getNCLists(self):
+		return self._ncLists
+	
+	def reset(self):
+		self.currentChrIndex = 0
+		self.currentReader   = None
+
+	def gotoAddress(self, address):
+		self.currentReader.gotoAddress(address)
+
+	def getCurrentAddress(self):
+		return self.getCurrentTranscriptAddress()
+
+	def getCurrentTranscriptAddress(self):
+		if self.currentReader == None:
+			return 0
+		return self.currentReader.getCurrentTranscriptAddress()
+
+	def getNextTranscript(self):
+		if self.currentReader == None:
+			self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[0]])
+		transcript = self.currentReader.getNextTranscript()
+		if transcript == False:
+			self.currentChrIndex += 1
+			if self.currentChrIndex >= len(self.chromosomes):
+				return None
+			self.currentReader = NCListFileUnpickle(self.fileNames[self.chromosomes[self.currentChrIndex]])
+			transcript = self.currentReader.getNextTranscript()
+		return transcript
+
+	def getInfos(self):
+		self.size = 0
+		self.reset()
+		progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9)
+		transcript = self.getNextTranscript()
+		for transcript in self.getIterator():
+			self.size += transcript.getSize()
+			progress.inc()
+		progress.done()
+		self.reset()
+
+	def getNbTranscripts(self):
+		return self.nbElements