annotate SMART/Java/Python/GetIntersection.py @ 62:8c42a6d7ffd4

Added simple test BED file.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2011
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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 GetIntersection(object):

	def __init__(self, verbosity):
		self.verbosity              = verbosity
		self.nbQueries              = 0
		self.nbRefs	                = 0
		self.nbWritten              = 0
		self.bins	                = {}

	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 loadRef(self):
		progress = UnlimitedProgress(10000, "Reading references", self.verbosity)
		for transcript in self.refParser.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)
			self.nbRefs += 1
			progress.inc()
		progress.done()

	def _compareTranscript(self, queryTranscript):
		queryChromosome = queryTranscript.getChromosome()
		if queryChromosome not in self.bins:
			return None
		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]:
					newTranscript = queryTranscript.getIntersection(refTranscript)
					if newTranscript != None:
						overlaps.append(newTranscript)
		if not overlaps:
			return None
		newTranscript = overlaps[0]
		for transcript in overlaps[1:]:
			newTranscript.merge(transcript)
		return newTranscript

	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
			newTranscript = self._compareTranscript(queryTranscript)
			if newTranscript != None:
				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" % (self.nbWritten)

	def run(self):
		self.loadRef()
		self.compare()
		self.displayResults()

if __name__ == "__main__":
	
	description = "Get Intersection v1.0.0: Shrink the first data set so that all bases covered by the first data set is also covered by the second data set. [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("-v", "--verbosity",      dest="verbosity",	   action="store",      default=1,     type="int",	 help="trace level [format: int]")
	(options, args) = parser.parse_args()

	gi = GetIntersection(options.verbosity)
	gi.setQueryFile(options.inputFileName1, options.format1)
	gi.setReferenceFile(options.inputFileName2, options.format2)
	gi.setOutputFile(options.outputFileName)
	gi.run()