--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/CompareOverlapping.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,491 @@
+#! /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.
+#
+import os, struct, time, random
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.Gff3Writer import Gff3Writer
+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.NCListHandler import NCListHandler
+from SMART.Java.Python.ncList.ConvertToNCList import ConvertToNCList
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+from SMART.Java.Python.misc import Utils
+try:
+	import cPickle as pickle
+except:
+	import pickle
+
+REFERENCE = 0
+QUERY = 1
+TYPES = (REFERENCE, QUERY)
+TYPETOSTRING = {0: "reference", 1: "query"}
+
+class CompareOverlapping(object):
+
+	def __init__(self, verbosity = 1):
+		self._outputFileName		   = "outputOverlaps.gff3"
+		self._iWriter				   = None
+		self._nbOverlappingQueries	   = 0
+		self._nbOverlaps			   = 0
+		self._nbLines				   = {REFERENCE: 0, QUERY: 0}
+		self._verbosity				   = verbosity
+		self._ncLists				   = {}
+		self._cursors				   = {}
+		self._splittedFileNames		   = {}
+		self._nbElements			   = {}
+		self._nbElementsPerChromosome  = {}
+		self._inputFileNames		   = {REFERENCE: None,  QUERY: None}
+		self._inputFileFormats		   = {REFERENCE: None,  QUERY: None}
+		self._starts				   = {REFERENCE: None, QUERY: None}
+		self._ends					   = {REFERENCE: None, QUERY: None}
+		self._fivePrimes			   = {REFERENCE: None, QUERY: None}
+		self._threePrimes			   = {REFERENCE: None, QUERY: None}
+		self._ncListHandlers		   = {REFERENCE: None,  QUERY: None}
+		self._convertedFileNames	   = {REFERENCE: False, QUERY: False}
+		self._sorted                   = False
+		self._index                    = False
+		self._introns				   = False
+		self._antisense				   = False
+		self._colinear				   = False
+		self._invert				   = False
+		self._distance				   = 0
+		self._minOverlap			   = 1
+		self._pcOverlap				   = None
+		self._included				   = False
+		self._including				   = False
+		self._outputNotOverlapping	   = False
+		self._tmpRefFileName		   = None
+		self._currentQueryTranscript   = None
+		self._currentOrQueryTranscript = None
+		self._currentExQueryTranscript = None
+		self._randInt				   = random.randint(0, 100000)
+		
+	def __del__(self):
+		for fileName in [self._tmpRefFileName] + self._convertedFileNames.values():
+			if fileName != None and os.path.exists(fileName):
+				os.remove(fileName)
+
+	def close(self):
+		self._iWriter.close()
+		
+	def setInput(self, fileName, format, type):
+		chooser = ParserChooser(self._verbosity)
+		chooser.findFormat(format)
+		self._inputFileNames[type]   = fileName
+		self._inputFileFormats[type] = format
+		
+	def setOutput(self, outputFileName):
+		if outputFileName != '':
+			self._outputFileName = outputFileName
+		self._iWriter = Gff3Writer(self._outputFileName)
+
+	def setSorted(self, sorted):
+		self._sorted = sorted
+
+	def setIndex(self, index):
+		self._index = index
+
+	def restrictToStart(self, distance, type):
+		self._starts[type] = distance
+		
+	def restrictToEnd(self, distance, type):
+		self._ends[type] = distance
+		
+	def extendFivePrime(self, distance, type):
+		self._fivePrimes[type] = distance
+		
+	def extendThreePrime(self, distance, type):
+		self._threePrimes[type] = distance
+
+	def acceptIntrons(self, boolean):
+		self._introns = boolean
+
+	def getAntisenseOnly(self, boolean):
+		self._antisense = boolean
+		
+	def getColinearOnly(self, boolean):
+		self._colinear = boolean
+
+	def getInvert(self, boolean):
+		self._invert = boolean
+
+	def setMaxDistance(self, distance):
+		self._distance = distance
+
+	def setMinOverlap(self, overlap):
+		self._minOverlap = overlap
+
+	def setPcOverlap(self, overlap):
+		self._pcOverlap = overlap
+
+	def setIncludedOnly(self, boolean):
+		self._included = boolean
+		
+	def setIncludingOnly(self, boolean):
+		self._including = boolean
+
+	def includeNotOverlapping(self, boolean):
+		self._outputNotOverlapping = boolean
+		
+	def transformTranscript(self, transcript, type):
+		if self._starts[type] != None:
+			transcript.restrictStart(self._starts[type])
+		if self._ends[type] != None:
+			transcript.restrictEnd(self._ends[type])
+		if self._fivePrimes[type] != None:
+			transcript.extendStart(self._fivePrimes[type])
+		if self._threePrimes[type] != None:
+			transcript.extendEnd(self._threePrimes[type])
+		if self._introns:
+			transcript.exons = []
+		if type == REFERENCE and self._distance > 0:
+			transcript.extendExons(self._distance)
+		return transcript
+
+	def extendQueryTranscript(self, transcript):
+		self._currentExQueryTranscript = Transcript()
+		self._currentExQueryTranscript.copy(transcript)
+		if self._fivePrimes[QUERY] != None:
+			self._currentExQueryTranscript.extendStart(self._fivePrimes[QUERY])
+		if self._threePrimes[QUERY] != None:
+			self._currentExQueryTranscript.extendEnd(self._threePrimes[QUERY])
+		transcript.exons = []
+
+	def createTmpRefFile(self):
+		self._tmpRefFileName = "tmp_ref_%d.pkl" % (self._randInt)
+		if "SMARTTMPPATH" in os.environ:
+			self._tmpRefFileName = os.path.join(os.environ["SMARTTMPPATH"], self._tmpRefFileName)
+		chooser = ParserChooser(self._verbosity)
+		chooser.findFormat(self._inputFileFormats[REFERENCE])
+		parser = chooser.getParser(self._inputFileNames[REFERENCE])
+		writer = NCListFilePickle(self._tmpRefFileName, self._verbosity)
+		for transcript in parser.getIterator():
+			transcript = self.transformTranscript(transcript, REFERENCE)
+			writer.addTranscript(transcript)
+		writer.close()
+		self._inputFileNames[REFERENCE]   = self._tmpRefFileName
+		self._inputFileFormats[REFERENCE] = "pkl"
+
+	def createNCLists(self):
+		self._ncLists = dict([type, {}] for type in TYPES)
+		self._indices = dict([type, {}] for type in TYPES)
+		self._cursors = dict([type, {}] for type in TYPES)
+		for type in TYPES:
+			if self._verbosity > 2:
+				print "Creating %s NC-list..." % (TYPETOSTRING[type])
+			self._convertedFileNames[type] = "%s_%d_%d.ncl" % (self._inputFileNames[type], self._randInt, type)
+			ncLists = ConvertToNCList(self._verbosity)
+			ncLists.setInputFileName(self._inputFileNames[type], self._inputFileFormats[type])
+			ncLists.setOutputFileName(self._convertedFileNames[type])
+			ncLists.setSorted(self._sorted)
+			if type == REFERENCE and self._index:
+				ncLists.setIndex(True)
+			ncLists.run()
+			self._ncListHandlers[type] = NCListHandler(self._verbosity)
+			self._ncListHandlers[type].setFileName(self._convertedFileNames[type])
+			self._ncListHandlers[type].loadData()
+			self._nbLines[type]					= self._ncListHandlers[type].getNbElements()
+			self._nbElementsPerChromosome[type] = self._ncListHandlers[type].getNbElementsPerChromosome()
+			self._ncLists[type]					= self._ncListHandlers[type].getNCLists()
+			for chromosome, ncList in self._ncLists[type].iteritems():
+				self._cursors[type][chromosome] = NCListCursor(None, ncList, 0, self._verbosity)
+				if type == REFERENCE and self._index:
+					self._indices[REFERENCE][chromosome] = ncList.getIndex()
+			if self._verbosity > 2:
+				print "	...done"
+
+	def compare(self):
+		nbSkips, nbMoves   = 0, 0
+		previousChromosome = None
+		done			   = False
+		refNCList		   = None
+		queryNCList		   = None
+		startTime		   = time.time()
+		progress		   = Progress(len(self._ncLists[QUERY].keys()), "Checking overlap", self._verbosity)
+		for chromosome, queryNCList in self._ncLists[QUERY].iteritems():
+			queryParser = self._ncListHandlers[QUERY].getParser(chromosome)
+			queryNCList = self._ncLists[QUERY][chromosome]
+			queryCursor = self._cursors[QUERY][chromosome]
+			if chromosome != previousChromosome:
+				skipChromosome		= False
+				previousChromosome  = chromosome
+				if chromosome not in self._ncLists[REFERENCE]:
+					if self._outputNotOverlapping:
+						while not queryCursor.isOut():
+							self._currentQueryTranscript = queryCursor.getTranscript()
+							self._writeIntervalInNewGFF3({})
+							if queryCursor.hasChildren():
+								queryCursor.moveDown()
+							else:
+								queryCursor.moveNext()
+					progress.inc()
+					continue
+				refNCList = self._ncLists[REFERENCE][chromosome]
+				refCursor = self._cursors[REFERENCE][chromosome]
+			while True:
+				self._currentOrQueryTranscript = queryCursor.getTranscript()
+				self._currentQueryTranscript = Transcript()
+				self._currentQueryTranscript.copy(self._currentOrQueryTranscript)
+				self._currentQueryTranscript = self.transformTranscript(self._currentQueryTranscript, QUERY)
+				self.extendQueryTranscript(self._currentOrQueryTranscript)
+				newRefLaddr = self.checkIndex(refCursor)
+				if newRefLaddr != None:
+					nbMoves += 1
+					refCursor.setLIndex(newRefLaddr)
+					done = False
+				refCursor, done, unmatched = self.findOverlapIter(refCursor, done)
+				if refCursor.isOut():
+					if not self._invert and not self._outputNotOverlapping:
+						break
+				if (unmatched and not self._invert and not self._outputNotOverlapping) or not queryCursor.hasChildren():
+					queryCursor.moveNext()
+					nbSkips += 1
+				else:
+					queryCursor.moveDown()
+				if queryCursor.isOut():
+					break
+			progress.inc()
+		progress.done()
+		endTime = time.time()
+		self._timeSpent = endTime - startTime
+		if self._verbosity >= 10:
+			print "# skips:   %d" % (nbSkips)
+			print "# moves:   %d" % (nbMoves)
+
+	def findOverlapIter(self, cursor, done):
+		chromosome = self._currentQueryTranscript.getChromosome()
+		matched	= False
+		if chromosome not in self._ncLists[REFERENCE]:
+			return None, False, True
+		ncList = self._ncLists[REFERENCE][chromosome]
+		overlappingNames = {}
+		nextDone = False
+		firstOverlapLAddr = NCListCursor(cursor)
+		firstOverlapLAddr.setLIndex(-1)
+		if cursor.isOut():
+			self._writeIntervalInNewGFF3(overlappingNames)
+			return firstOverlapLAddr, False, True
+		parentCursor = NCListCursor(cursor)
+		parentCursor.moveUp()
+		firstParentAfter = False
+		while not parentCursor.isOut(): 
+			if self.isOverlapping(parentCursor) == 0:
+				matched = True
+				if self._checkOverlap(parentCursor.getTranscript()):
+					overlappingNames.update(self._extractID(parentCursor.getTranscript()))
+				if firstOverlapLAddr.isOut():
+					firstOverlapLAddr.copy(parentCursor)
+					nextDone = True 
+			elif self.isOverlapping(parentCursor) == 1:
+				firstParentAfter = NCListCursor(parentCursor)
+			parentCursor.moveUp()
+		if firstParentAfter:
+			written = self._writeIntervalInNewGFF3(overlappingNames)
+			return firstParentAfter, False, not written if self._invert else not matched
+		#This loop finds the overlaps with currentRefLAddr.#
+		while True:
+			parentCursor = NCListCursor(cursor)
+			parentCursor.moveUp()
+			#In case: Query is on the right of the RefInterval and does not overlap.
+			overlap = self.isOverlapping(cursor)
+			if overlap == -1:
+				cursor.moveNext()
+			#In case: Query overlaps with RefInterval.	
+			elif overlap == 0:
+				matched = True
+				if self._checkOverlap(cursor.getTranscript()):
+					overlappingNames.update(self._extractID(cursor.getTranscript()))
+				if firstOverlapLAddr.compare(parentCursor):
+					firstOverlapLAddr.copy(cursor)
+					nextDone = True
+				if done:
+					cursor.moveNext()
+				else:
+					if not cursor.hasChildren():
+						cursor.moveNext()
+						if cursor.isOut():
+							break
+					else:
+						cursor.moveDown()
+			#In case: Query is on the left of the RefInterval and does not overlap.		
+			else:
+				if firstOverlapLAddr.isOut() or firstOverlapLAddr.compare(parentCursor):
+					firstOverlapLAddr.copy(cursor)
+					nextDone = False # new
+				break
+			
+			done = False
+			if cursor.isOut():
+				break
+		written = self._writeIntervalInNewGFF3(overlappingNames)
+		return firstOverlapLAddr, nextDone, not written if self._invert else not matched
+	
+	def isOverlapping(self, refTranscript):
+		if (self._currentExQueryTranscript.getStart() <= refTranscript.getEnd() and self._currentExQueryTranscript.getEnd() >= refTranscript.getStart()):
+			return 0   
+		if self._currentExQueryTranscript.getEnd() < refTranscript.getStart():
+			return 1
+		return -1
+
+	def checkIndex(self, cursor):
+		if not self._index:
+			return None
+		if cursor.isOut():
+			return None
+		chromosome = self._currentExQueryTranscript.getChromosome()
+		nextLIndex = self._indices[REFERENCE][chromosome].getIndex(self._currentExQueryTranscript)
+		if nextLIndex == None:
+			return None
+		ncList		 = self._ncLists[REFERENCE][chromosome]
+		nextGffAddress = ncList.getRefGffAddr(nextLIndex)
+		thisGffAddress = cursor.getGffAddress()
+		if nextGffAddress > thisGffAddress:
+			return nextLIndex
+		return None
+		
+	def _writeIntervalInNewGFF3(self, names):
+		nbOverlaps = 0
+		for cpt in names.values():
+			nbOverlaps += cpt
+		self._nbOverlappingQueries += 1		      if Utils.xor(names, self._invert) else 0
+		self._nbOverlaps		   += nbOverlaps  if Utils.xor(names, self._invert) else 0
+		if names:
+			self._currentQueryTranscript.setTagValue("overlapWith", ",".join(names))
+			self._currentQueryTranscript.setTagValue("nbOverlaps", nbOverlaps)
+			if self._invert:
+				return False
+		else:
+			if self._outputNotOverlapping:
+				self._currentQueryTranscript.setTagValue("nbOverlaps", 0)
+			elif not self._invert:
+				return False
+		self._iWriter.addTranscript(self._currentQueryTranscript)
+		self._iWriter.write()
+		return True
+		
+	def _extractID(self, transcript):
+		id		 = transcript.getTagValue("ID")		      if "ID"		  in transcript.getTagNames() else transcript.getUniqueName()
+		nbElements = transcript.getTagValue("nbElements") if "nbElements" in transcript.getTagNames() else 1
+		return {id: float(nbElements)}
+
+	def _checkOverlap(self, refTranscript):
+		if self._currentQueryTranscript.getDistance(refTranscript) > self._distance:
+			return False
+		minOverlap = self._minOverlap
+		if self._pcOverlap != None:
+			minOverlap = max(self._minOverlap, self._currentQueryTranscript.getSize() / 100.0 * self._pcOverlap)
+		if not self._currentQueryTranscript.overlapWith(refTranscript, minOverlap):
+			return False
+		if self._antisense and self._currentQueryTranscript.getDirection() == refTranscript.getDirection():
+			return False
+		if self._colinear and self._currentQueryTranscript.getDirection() != refTranscript.getDirection():
+			return False
+		if self._included and not refTranscript.include(self._currentQueryTranscript):
+			return False
+		if self._including and not self._currentQueryTranscript.include(refTranscript):
+			return False
+		if self._introns:
+			return True
+		return self._currentQueryTranscript.overlapWithExon(refTranscript, minOverlap)
+		
+	def run(self):
+		self.createTmpRefFile()
+		self.createNCLists()
+		self.compare()
+		self.close()
+		if self._verbosity > 0:
+			print "# queries: %d" % (self._nbLines[QUERY])
+			print "# refs:	  %d" % (self._nbLines[REFERENCE])
+			print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps)
+			print "time: 	  %ds" % (self._timeSpent)
+
+
+if __name__ == "__main__":
+	description = "Compare Overlapping v1.0.4: Get the data which overlap with a reference set. [Category: Data Comparison]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input1",		      dest="inputFileName1", action="store",					 type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format1",		  dest="format1",		 action="store",					 type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+	parser.add_option("-j", "--input2",		      dest="inputFileName2", action="store",					 type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+	parser.add_option("-g", "--format2",		  dest="format2",		 action="store",					 type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+	parser.add_option("-o", "--output",		      dest="output",		 action="store",	  default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+	parser.add_option("-D", "--index",	          dest="index",	         action="store_true", default=False,	            help="add an index to the reference file (faster but more memory) [format: boolean] [default: False]")
+	parser.add_option("-r", "--sorted",	          dest="sorted",	     action="store_true", default=False,	            help="input files are already sorted [format: boolean] [default: False]")
+	parser.add_option("-S", "--start1",		      dest="start1",		 action="store",	  default=None,  type="int",	help="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]")
+	parser.add_option("-s", "--start2",		      dest="start2",		 action="store",	  default=None,  type="int",	help="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]")
+	parser.add_option("-U", "--end1",			  dest="end1",		     action="store",	  default=None,  type="int",	help="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]")
+	parser.add_option("-u", "--end2",			  dest="end2",		     action="store",	  default=None,  type="int",	help="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]")
+	parser.add_option("-t", "--intron",		      dest="introns",		 action="store_true", default=False,				help="also report introns [format: bool] [default: false]")
+	parser.add_option("-E", "--5primeExtension1", dest="fivePrime1",	 action="store",	  default=None,  type="int",	help="extension towards 5' in file 1 [format: int]")
+	parser.add_option("-e", "--5primeExtension2", dest="fivePrime2",	 action="store",	  default=None,  type="int",	help="extension towards 5' in file 2 [format: int]")
+	parser.add_option("-N", "--3primeExtension1", dest="threePrime1",	 action="store",	  default=None,  type="int",	help="extension towards 3' in file 1 [format: int]")
+	parser.add_option("-n", "--3primeExtension2", dest="threePrime2",	 action="store",	  default=None,  type="int",	help="extension towards 3' in file 2 [format: int]")
+	parser.add_option("-c", "--colinear",		  dest="colinear",		 action="store_true", default=False,				help="colinear only [format: bool] [default: false]")
+	parser.add_option("-a", "--antisense",		  dest="antisense",		 action="store_true", default=False,				help="antisense only [format: bool] [default: false]")
+	parser.add_option("-d", "--distance",		  dest="distance",	     action="store",	  default=0,	 type="int",	help="accept some distance between query and reference [format: int]")
+	parser.add_option("-k", "--included",		  dest="included",	     action="store_true", default=False,				help="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]")
+	parser.add_option("-K", "--including",		  dest="including",	     action="store_true", default=False,				help="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]")
+	parser.add_option("-m", "--minOverlap",		  dest="minOverlap",	 action="store",	  default=1,	 type="int",	help="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]")
+	parser.add_option("-p", "--pcOverlap",		  dest="pcOverlap",	     action="store",	  default=None,  type="int",	help="minimum percentage of nucleotides to overlap to declare an overlap [format: int]")
+	parser.add_option("-O", "--notOverlapping",   dest="notOverlapping", action="store_true", default=False,				help="also output not overlapping data [format: bool] [default: false]")
+	parser.add_option("-x", "--exclude",		  dest="exclude",		 action="store_true", default=False,				help="invert the match [format: bool] [default: false]")
+	parser.add_option("-v", "--verbosity",		  dest="verbosity",		 action="store",	  default=1,	 type="int",	help="trace level [format: int]")
+	(options, args) = parser.parse_args()
+
+	co = CompareOverlapping(options.verbosity)
+	co.setInput(options.inputFileName1, options.format1, QUERY)
+	co.setInput(options.inputFileName2, options.format2, REFERENCE)
+	co.setOutput(options.output)
+	co.setSorted(options.sorted)
+	co.setIndex(options.index)
+	co.restrictToStart(options.start1, QUERY)
+	co.restrictToStart(options.start2, REFERENCE)
+	co.restrictToEnd(options.end1, QUERY)
+	co.restrictToEnd(options.end2, REFERENCE)
+	co.extendFivePrime(options.fivePrime1, QUERY)
+	co.extendFivePrime(options.fivePrime2, REFERENCE)
+	co.extendThreePrime(options.threePrime1, QUERY)
+	co.extendThreePrime(options.threePrime2, REFERENCE)
+	co.acceptIntrons(options.introns)
+	co.getAntisenseOnly(options.antisense)
+	co.getColinearOnly(options.colinear)
+	co.getInvert(options.exclude)
+	co.setMaxDistance(options.distance)
+	co.setMinOverlap(options.minOverlap)
+	co.setPcOverlap(options.pcOverlap)
+	co.setIncludedOnly(options.included)
+	co.setIncludingOnly(options.including)
+	co.includeNotOverlapping(options.notOverlapping)
+	co.run()