annotate SMART/Java/Python/CompareOverlappingSmallRef.py @ 10:c081f25e1572

Updated CompareOverlappingSmallRef.py

#! /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".
# 
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# modify and redistribute granted by the license, users are provided only
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# economic rights, and the successive licensors have only limited
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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()