annotate smart_toolShed/SMART/Java/Python/CompareOverlappingSmallRef.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /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
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# The fact that you are presently reading this means that you have had
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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.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 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
		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):
		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("-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.setInvert(options.exclude)
	cosr.setInvert(options.exclude)
	cosr.run()