diff smart_toolShed/SMART/Java/Python/ncList/NCListFilePickle.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/ncList/NCListFilePickle.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,123 @@
+#! /usr/bin/env python
+#
+# 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
+# "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.
+#
+
+try:
+	 import cPickle as pickle
+except:
+	 import pickle
+from SMART.Java.Python.structure.Transcript import Transcript
+
+
+class NCListFilePickle(object):
+	
+	def __init__(self, fileName, verbosity = 1):
+		self.fileName  = fileName
+		self.handle	= open(fileName, "wb")
+		self.verbosity = verbosity
+
+	def __del__(self):
+		if self.handle != None:
+			self.handle.close()
+	
+	def addTranscript(self, transcript):
+		pickle.dump(transcript, self.handle, -1)
+
+	def write(self):
+		pass
+
+	def close(self):
+		self.__del__()
+
+
+class NCListFileUnpickle(object):
+		
+	def __init__(self, fileName, verbosity = 1):
+		self.handle		   = open(fileName, "rb")
+		self.verbosity	   = verbosity
+		self.initAddress   = 0
+		self.address	   = self.initAddress
+		self.nbTranscripts = None
+		self.fileName	   = fileName
+		self.over		   = False
+		self.chromosome    = None
+
+	def __del__(self):
+		if self.handle != None:
+			self.handle.close()
+
+	def reset(self):
+		self.handle.seek(0)
+		self.initAddress = 0
+
+	def setChromosome(self, chromosome):
+		self.chromosome = chromosome
+	
+	def getNbTranscripts(self):
+		if self.nbTranscripts != None:
+			return self._nbTranscripts
+		self.nbTranscripts = 0
+		for transcript in self.getIterator():
+			self_nbTranscripts += 1
+		return self.nbTranscripts
+
+	def gotoAddress(self, address):
+		self.handle.seek(address)
+		self.address = address
+
+	def getNextTranscript(self):
+		self.address = self.handle.tell()
+		try:
+			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):
+		self.gotoAddress(self.initAddress)
+		while True:
+			transcript = self.getNextTranscript()
+			if not transcript:
+				self.over = True
+				return
+			yield transcript
+
+	def setInitAddress(self, address):
+		self.initAddress = address
+
+	def getCurrentTranscriptAddress(self):
+		return self.address
+
+	def isOver(self):
+		return self.over