annotate SMART/Java/Python/CompareOverlappingSmallQuery.py @ 9:1eb55963fe39

Updated CompareOverlappingSmall*.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".
# 
# 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 CompareOverlappingSmallQuery(object):

	def __init__(self, verbosity):
		self.verbosity      = verbosity
		self.tableNames     = {}
		self.nbQueries      = 0
		self.nbRefs	        = 0
		self.nbWritten      = 0
		self.nbOverlaps     = 0
		self.distance       = None
		self.invert         = False
		self.antisense      = False
		self.collinear      = False
		self.pcOverlapQuery = False
		self.pcOverlapRef   = False
		self.minOverlap     = False
		self.included       = False
		self.including      = False
		self.bins	        = {}
		self.overlaps       = {}
		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 setInvert(self, boolean):
		self.invert = boolean

	def setCollinear(self, boolean):
		self.collinear = boolean

	def setAntisense(self, boolean):
		self.antisense = boolean

	def setMinPercentOverlap(self, pcOverlapQuery, pcOverlapRef):
		self.pcOverlapQuery = pcOverlapQuery
		self.pcOverlapRef   = pcOverlapRef

	def setMinOverlap(self, minOverlap):
		self.minOverlap = minOverlap

	def setInclude(self, included, including):
		self.included  = included
		self.including = including

	def includeNotOverlapping(self, boolean):
		self.notOverlapping = boolean

	def loadQuery(self):
		progress = UnlimitedProgress(10000, "Reading queries", self.verbosity)
		for transcript in self.queryParser.getIterator():
			if transcript.__class__.__name__ == "Mapping":
				transcript = transcript.getTranscript()
			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)
			if self.notOverlapping or self.invert:
				self.overlaps[transcript] = {}
			self.nbQueries += 1
			progress.inc()
		progress.done()

	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 refTranscript.include(queryTranscript):
			return False
		if self.including and not queryTranscript.include(refTranscript):
			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 _alterTranscript(self, transcript, type):
		if type == REFERENCE:
			if self.distance != None:
				transcript.extendExons(self.distance)
		return transcript

	def _compareTranscript(self, refTranscript):
		refChromosome = refTranscript.getChromosome()
		if refChromosome not in self.bins:
			return []
		refStart = refTranscript.getStart()
		refEnd   = refTranscript.getEnd()
		bins	 = getOverlappingBins(refStart, refEnd)
		for binRange in bins:
			for bin in range(binRange[0], binRange[1]+1):
				if bin not in self.bins[refChromosome]:
					continue
				for queryTranscript in self.bins[refChromosome][bin]:
					if self._compareTwoTranscripts(queryTranscript, refTranscript):
						if queryTranscript not in self.overlaps:
							self.overlaps[queryTranscript] = {}
						nbElements = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
						self.overlaps[queryTranscript][refTranscript.getName()] = int(float(refTranscript.getTagValue("nbElements"))) if "nbElements" in refTranscript.getTagNames() else 1
						self.nbOverlaps += nbElements

	def _updateTranscript(self, queryTranscript):
		overlaps = self.overlaps[queryTranscript]
		queryTranscript.setTagValue("nbOverlaps", sum(overlaps.values()))
		if overlaps:
			queryTranscript.setTagValue("overlapsWith", "--".join(overlaps.keys())[:100])
		return queryTranscript

	def compare(self):
		progress = UnlimitedProgress(10000, "Comparing references", self.verbosity)
		for refTranscript in self.refParser.getIterator():
			if refTranscript.__class__.__name__ == "Mapping":
				refTranscript = refTranscript.getTranscript()
			refTranscript = self._alterTranscript(refTranscript, REFERENCE)
			self._compareTranscript(refTranscript)
			self.nbRefs += 1
			progress.inc()
		progress.done()

	def printResults(self):
		for transcript in self.overlaps:
			if not self.invert or not self.overlaps[transcript]:
				if not self.invert:
					transcript = self._updateTranscript(transcript)
				self.writer.addTranscript(transcript)
				self.nbWritten += 1
		self.writer.close()

	def displayResults(self):
		if self.verbosity:
			print "# queries:  %d" % (self.nbQueries)
			print "# refs:     %d" % (self.nbRefs)
			print "# written:  %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps)

	def run(self):
		self.loadQuery()
		self.compare()
		self.printResults()
		self.displayResults()

if __name__ == "__main__":
	
	description = "Compare Overlapping Small Query v1.0.1: Provide the queries that overlap with a reference, when the query 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()

	cosq = CompareOverlappingSmallQuery(options.verbosity)
	cosq.setQueryFile(options.inputFileName1, options.format1)
	cosq.setReferenceFile(options.inputFileName2, options.format2)
	cosq.setOutputFile(options.outputFileName)
	cosq.includeNotOverlapping(options.notOverlapping)
	cosq.setDistance(options.distance)
	cosq.setCollinear(options.collinear)
	cosq.setAntisense(options.antisense)
	cosq.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef)
	cosq.setMinOverlap(options.minOverlap)
	cosq.setInclude(options.included, options.including)
	cosq.setInvert(options.exclude)
	cosq.run()