--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/CompareOverlappingSmallRef.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,250 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2011
+# 
+# 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.
+#
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Mapping import Mapping
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+MINBIN = 3
+MAXBIN = 7
+REFERENCE = 0
+QUERY = 1
+
+def getBin(start, end):
+	for i in range(MINBIN, MAXBIN + 1):
+		binLevel = 10 ** i
+		if int(start / binLevel) == int(end / binLevel):
+			return int(i * 10 ** (MAXBIN + 1) + int(start / binLevel))
+	return int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+
+def getOverlappingBins(start, end):
+	array	= []
+	bigBin = int((MAXBIN + 1) * 10 ** (MAXBIN + 1))
+	for i in range(MINBIN, MAXBIN + 1):
+		binLevel = 10 ** i
+		array.append((int(i * 10 ** (MAXBIN + 1) + int(start / binLevel)), int(i * 10 ** (MAXBIN + 1) + int(end / binLevel))))
+	array.append((bigBin, bigBin))
+	return array
+
+
+class CompareOverlappingSmallRef(object):
+
+	def __init__(self, verbosity):
+		self.verbosity      = verbosity
+		self.tableNames     = {}
+		self.nbQueries      = 0
+		self.nbRefs	        = 0
+		self.nbWritten      = 0
+		self.nbOverlaps     = 0
+		self.invert         = False
+		self.antisense      = False
+		self.collinear      = False
+		self.distance       = None
+		self.minOverlap     = False
+		self.pcOverlapQuery = False
+		self.pcOverlapRef   = False
+		self.included       = False
+		self.including      = False
+		self.bins	        = {}
+		self.notOverlapping = False
+
+	def setReferenceFile(self, fileName, format):
+		chooser = ParserChooser(self.verbosity)
+		chooser.findFormat(format)
+		self.refParser = chooser.getParser(fileName)
+
+	def setQueryFile(self, fileName, format):
+		chooser = ParserChooser(self.verbosity)
+		chooser.findFormat(format)
+		self.queryParser = chooser.getParser(fileName)
+
+	def setOutputFile(self, fileName):
+		self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+
+	def setDistance(self, distance):
+		self.distance = distance
+
+	def setCollinear(self, boolean):
+		self.collinear = boolean
+
+	def setAntisense(self, boolean):
+		self.antisense = boolean
+
+	def setInvert(self, boolean):
+		self.invert = boolean
+
+	def setMinPercentOverlap(self, pcOverlapQuery, pcOverlapRef):
+		self.pcOverlapQuery = pcOverlapQuery
+		self.pcOverlapRef   = pcOverlapRef
+
+	def setInclude(self, included, including):
+		self.included  = included
+		self.including = including
+
+	def includeNotOverlapping(self, boolean):
+		self.notOverlapping = boolean
+
+	def loadRef(self):
+		progress = UnlimitedProgress(10000, "Reading references", self.verbosity)
+		for transcript in self.refParser.getIterator():
+			if transcript.__class__.__name__ == "Mapping":
+				transcript = transcript.getTranscript()
+			transcript = self._alterTranscript(transcript, REFERENCE)
+			chromosome = transcript.getChromosome()
+			bin		   = getBin(transcript.getStart(), transcript.getEnd())
+			if chromosome not in self.bins:
+				self.bins[chromosome] = {}
+			if bin not in self.bins[chromosome]:
+				self.bins[chromosome][bin] = []
+			self.bins[chromosome][bin].append(transcript)
+			self.nbRefs += 1
+			progress.inc()
+		progress.done()
+
+	def _alterTranscript(self, transcript, type):
+		if type == REFERENCE:
+			if self.distance != None:
+				transcript.extendExons(self.distance)
+		return transcript
+
+	def _compareTwoTranscripts(self, queryTranscript, refTranscript):
+		if not queryTranscript.overlapWithExon(refTranscript):
+			return False
+		if self.collinear and queryTranscript.getDirection() != refTranscript.getDirection():
+			return False
+		if self.antisense and queryTranscript.getDirection() == refTranscript.getDirection():
+			return False
+		if self.included and not queryTranscript.isIncluded(refTranscript):
+			return False
+		if self.including and not refTranscript.isIncluded(queryTranscript):
+			return False
+		querySize = queryTranscript.getSize()
+		if self.pcOverlapQuery and not queryTranscript.overlapWithExon(refTranscript, int(querySize * self.pcOverlapQuery / 100.0)):
+			return False
+		refSize = refTranscript.getSize()
+		if self.pcOverlapRef and not queryTranscript.overlapWithExon(refTranscript, int(refSize * self.pcOverlapRef / 100.0)):
+			return False
+		if self.minOverlap and not queryTranscript.overlapWithExon(refTranscript, self.minOverlap):
+			return False
+		return True
+
+	def _compareTranscript(self, queryTranscript):
+		queryChromosome = queryTranscript.getChromosome()
+		if queryChromosome not in self.bins:
+			return []
+		queryStart = queryTranscript.getStart()
+		queryEnd   = queryTranscript.getEnd()
+		bins	   = getOverlappingBins(queryStart, queryEnd)
+		overlaps   = {}
+		for binRange in bins:
+			for bin in range(binRange[0], binRange[1]+1):
+				if bin not in self.bins[queryChromosome]:
+					continue
+				for refTranscript in self.bins[queryChromosome][bin]:
+					if self._compareTwoTranscripts(queryTranscript, refTranscript):
+						nbElements = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
+						overlaps[refTranscript.getName()] = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
+						self.nbOverlaps += nbElements
+		return overlaps
+
+	def _updateTranscript(self, queryTranscript, overlaps):
+		queryTranscript.setTagValue("nbOverlaps", sum(overlaps.values()))
+		if overlaps:
+			queryTranscript.setTagValue("overlapsWith", "--".join(overlaps.keys())[:100])
+		return queryTranscript
+
+	def compare(self):
+		progress = UnlimitedProgress(10000, "Comparing queries", self.verbosity)
+		for queryTranscript in self.queryParser.getIterator():
+			if queryTranscript.__class__.__name__ == "Mapping":
+				queryTranscript = queryTranscript.getTranscript()
+			progress.inc()
+			self.nbQueries += 1
+			overlaps = self._compareTranscript(queryTranscript)
+			if self.notOverlapping or (overlaps and not self.invert) or (not overlaps and self.invert):
+				if not self.invert:
+					queryTranscript = self._updateTranscript(queryTranscript, overlaps)
+				self.writer.addTranscript(queryTranscript)
+				self.nbWritten += 1
+		progress.done()
+		self.writer.close()
+
+	def displayResults(self):
+		if self.verbosity > 0:
+			print "# queries:  %d" % (self.nbQueries)
+			print "# refs:     %d" % (self.nbRefs)
+			print "# written:  %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps)
+
+	def run(self):
+		self.loadRef()
+		self.compare()
+		self.displayResults()
+
+if __name__ == "__main__":
+	
+	description = "Compare Overlapping Small Reference v1.0.1: Provide the queries that overlap with a reference, when the reference is small. [Category: Data Comparison]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input1",	        dest="inputFileName1", action="store",			           type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format1",        dest="format1",		  action="store",			           type="string", help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-j", "--input2",	        dest="inputFileName2", action="store",			           type="string", help="reference input file [compulsory] [format: file in transcript format given by -g]")
+	parser.add_option("-g", "--format2",        dest="format2",		  action="store",			           type="string", help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-o", "--output",	        dest="outputFileName", action="store",			           type="string", help="output file [format: output file in GFF3 format]")
+	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("-d", "--distance",		dest="distance",	   action="store",	    default=0,	   type="int",	  help="accept some distance between query and reference [format: int]")
+	parser.add_option("-c", "--collinear",		dest="collinear",	   action="store_true", default=False,			 	  help="provide collinear features [format: bool] [default: false]")
+	parser.add_option("-a", "--antisense",		dest="antisense",	   action="store_true", default=False,			 	  help="provide antisense features [format: bool] [default: false]")
+	parser.add_option("-m", "--minOverlap",	    dest="minOverlap",     action="store",      default=False, type="int",	  help="min. #nt overlap [format: bool] [default: false]")
+	parser.add_option("-p", "--pcOverlapQuery",	dest="pcOverlapQuery", action="store",      default=False, type="int",	  help="min. % overlap of the query [format: bool] [default: false]")
+	parser.add_option("-P", "--pcOverlapRef",	dest="pcOverlapRef",   action="store",      default=False, type="int",    help="min. % overlap of the reference [format: bool] [default: false]")
+	parser.add_option("-k", "--included",		dest="included",	   action="store_true", default=False,			 	  help="provide query elements which are nested in reference elements [format: bool] [default: false]")
+	parser.add_option("-K", "--including",		dest="including",	   action="store_true", default=False,			 	  help="provide query elements in which reference elements are nested [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()
+
+	cosr = CompareOverlappingSmallRef(options.verbosity)
+	cosr.setQueryFile(options.inputFileName1, options.format1)
+	cosr.setReferenceFile(options.inputFileName2, options.format2)
+	cosr.setOutputFile(options.outputFileName)
+	cosr.includeNotOverlapping(options.notOverlapping)
+	cosr.setDistance(options.distance)
+	cosr.setAntisense(options.antisense)
+	cosr.setInclude(options.included, options.including)
+	cosr.setInvert(options.exclude)
+	cosr.setMinOverlap(options.minOverlap)
+	cosr.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
+	cosr.run()
+