--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/ConvertToNCList.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,172 @@
+#! /usr/bin/env python
+#
+# 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 random, os, time, shutil
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+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 NCListFilePickle, NCListFileUnpickle
+from SMART.Java.Python.ncList.FileSorter import FileSorter
+from SMART.Java.Python.ncList.NCListMerger import NCListMerger
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+try:
+   import cPickle as pickle
+except:
+   import pickle
+
+class ConvertToNCList(object):
+	
+	def __init__(self, verbosity = 1):
+		self._parsers				  = {}
+		self._sortedFileNames		  = {}
+		self._inputFileName		      = None
+		self._outputFileName		  = None
+		self._index				      = False
+		self._ncLists				  = {}
+		self._splittedFileNames	      = {}
+		self._nbElements			  = 0
+		self._nbElementsPerChromosome = {}
+		self._randomNumber			  = random.randint(0, 10000)
+		self._sorted                  = False
+		self._verbosity			      = verbosity
+		
+	def setInputFileName(self, fileName, format):
+		self._inputFileName = fileName
+		chooser = ParserChooser(self._verbosity)
+		chooser.findFormat(format)
+		self._parser = chooser.getParser(fileName)
+		
+	def setOutputFileName(self, fileName):
+		self._outputFileName = fileName
+		fileNameNoExtension  = os.path.splitext(fileName)[0]
+		baseName			 = "%s_%d" % (fileNameNoExtension, self._randomNumber)
+		self._directory	     = "%s_files" % (baseName)
+		if not os.path.exists(self._directory):
+			os.makedirs(self._directory)
+		self._sortedFileNames = os.path.join(self._directory, baseName)
+
+	def setIndex(self, boolean):
+		self._index = boolean
+
+	def setSorted(self, boolean):
+		self._sorted = boolean
+
+	def sortFile(self):
+		if self._verbosity > 2:
+			print "%s file %s..." % ("Rewriting" if self._sorted else "Sorting", self._inputFileName)
+		startTime = time.time()
+		fs = FileSorter(self._parser, self._verbosity-4)
+		fs.setPresorted(self._sorted)
+		fs.perChromosome(True)
+		fs.setOutputFileName(self._sortedFileNames)
+		fs.sort()
+		self._splittedFileNames	      = fs.getOutputFileNames()
+		self._nbElementsPerChromosome = fs.getNbElementsPerChromosome()
+		self._nbElements			  = fs.getNbElements()
+		endTime = time.time()
+		if self._verbosity > 2:
+			print "	...done (%ds)" % (endTime - startTime)
+			
+	def createNCLists(self):
+		self._ncLists = {}
+		if self._verbosity > 2:
+			print "Creating NC-list for %s..." % (self._inputFileName)
+		startTime = time.time()
+		for chromosome, fileName in self._splittedFileNames.iteritems():
+			if self._verbosity > 3:
+				print "  chromosome %s" % (chromosome)
+			ncList = NCList(self._verbosity)
+			if self._index:
+				ncList.createIndex(True)
+			ncList.setChromosome(chromosome)
+			ncList.setFileName(fileName)
+			ncList.setNbElements(self._nbElementsPerChromosome[chromosome])
+			ncList.buildLists()
+			self._ncLists[chromosome] = ncList
+		endTime = time.time()
+		if self._verbosity > 2:
+			print "	...done (%ds)" % (endTime - startTime)
+
+	def writeOutputFile(self):
+		merger = NCListMerger(self._verbosity)
+		merger.setFileName(self._outputFileName)
+		merger.addIndex(self._index)
+		merger.setNCLists(self._ncLists)
+		merger.merge()
+
+	def cleanFiles(self):
+		shutil.rmtree(self._directory)
+
+	def run(self):
+		self.sortFile()
+		self.createNCLists()
+		self.writeOutputFile()
+		self.cleanFiles()
+
+	def getSortedFileNames(self):
+		return self._splittedFileNames
+
+	def getNbElements(self):
+		return self._nbElements
+
+	def getNbElementsPerChromosome(self):
+		return self._nbElementsPerChromosome
+
+	def getNCLists(self):
+		return self._ncLists
+
+	def getTmpDirectory(self):
+		return self._directory
+
+
+if __name__ == "__main__":
+	description = "Convert To NC-List v1.0.0: Convert a mapping or transcript file into a NC-List. [Category: NC-List]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input",	   dest="inputFileName",  action="store",					  type="string",  help="Query input file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format",	   dest="format",		  action="store",					  type="string",  help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-d", "--index",	   dest="index",		  action="store_true", default=False,				  help="create an index [default: false] [format: boolean]")
+	parser.add_option("-o", "--output",	   dest="outputFileName", action="store",					  type="string",  help="Output file [compulsory] [format: output file in NCList format]")
+	parser.add_option("-s", "--sorted",	   dest="sorted",	      action="store_true", default=False,	              help="input file is already sorted [format: boolean] [default: False]")
+	parser.add_option("-v", "--verbosity", dest="verbosity",	  action="store",	   default=1,	  type="int",	  help="Trace level [format: int] [default: 1]")
+	(options, args) = parser.parse_args()
+	
+	ctncl = ConvertToNCList(options.verbosity)
+	ctncl.setInputFileName(options.inputFileName, options.format)
+	ctncl.setOutputFileName(options.outputFileName)
+	ctncl.setIndex(options.index)
+	ctncl.setSorted(options.sorted)
+	ctncl.run()
+