comparison smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithOneInterval.py @ 0:e0f8dcca02ed

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

0:e0f8dcca02ed

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
# 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.
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# In this respect, the user's attention is drawn to the risks associated
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# software by the user in light of its specific status of free software,
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import struct
import math
import os
from optparse import OptionParser
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.ncList.NCList import NCList
from SMART.Java.Python.ncList.FileSorter import FileSorter
from commons.core.parsing.ParserChooser import ParserChooser
from SMART.Java.Python.ncList.NCListCursor import NCListCursor
from SMART.Java.Python.structure.Transcript import Transcript

LONGSIZE = struct.calcsize('l')

class FindOverlapsWithOneInterval(object):
	
	def __init__(self, verbosity):
		self._sortedFileName   = None
		self._verbosity		= verbosity
		self._overlappingNames = []
		self._nbOverlaps	   = 0
		self._nbWritten		= 0
		
	def __del__(self):
		if self._sortedFileName and os.path.exists(self._sortedFileName):
			os.remove(self._sortedFileName)
	
	def close(self):
		self._iWriter.close()
		
	def setOutputFileName(self, fileName):
		self._iWriter = Gff3Writer(fileName)
		
	def setFileName(self, fileName, format):
		chooser = ParserChooser(self._verbosity)
		chooser.findFormat(format)
		self._parser		 = chooser.getParser(fileName)
		self._sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
		
	def setInterval(self, chromosome, start, end):
		self._chromosome = chromosome
		self._start	  = start
		self._end		= end
		self._transcript = Transcript()
		self._transcript.setChromosome(chromosome)
		self._transcript.setStart(start)
		self._transcript.setEnd(end)
		self._transcript.setDirection("+")
		
	def setTranscript(self, transcript):
		if transcript.__class__.__name__ == "Mapping":
			transcript = transcript.getTranscript()
		self._chromosome = transcript.getChromosome()
		self._start	  = transcript.getStart()
		self._end		= transcript.getEnd()
		self._transcript = transcript

	def prepareIntermediateFiles(self):
		fs = FileSorter(self._parser, self._verbosity-4)
		fs.selectChromosome(self._chromosome)
		fs.perChromosome(False)
		fs.setOutputFileName(self._sortedFileName)
		fs.sort()
		self._nbTotalLines = fs.getNbElements()
		self._nbLines	  = fs.getNbElementsPerChromosome()[self._chromosome]
			
	def createNCList(self):
		if self._verbosity > 2:
			print "Creating NC-list..."
		ncList = NCList(self._verbosity)
		ncList.createIndex(True)
		ncList.setChromosome(self._chromosome)
		ncList.setFileName(self._sortedFileName)
		ncList.setNbElements(self._nbTotalLines)
		ncList.buildLists()
		self.setNCList(ncList, ncList.getIndex())
		if self._verbosity > 2:
			print "	...done (%ds)" % (endTime - startTime)

	def setNCList(self, ncList, index):
		self._ncList = ncList
		self._indix  = index

	def binarySearch(self, cursor, startL, endL):
		if startL > endL:
			return None
		middleL = (startL + endL) / 2
		cursor.moveSibling(middleL)
		overlap = self.isOverlapping(cursor)
		if overlap == 0:
			if middleL == startL:
				return cursor
			else:
				return self.binarySearch(cursor, startL, middleL)
		if overlap == -1:
			return self.binarySearch(cursor, middleL + 1, endL)
		return self.binarySearch(cursor, startL, middleL - 1)

	def compare(self, cursor = None):
		self._ncList.openFiles()
		if cursor == None:
			dump   = True
			cursor = NCListCursor(None, self._ncList, 0, self._verbosity)
		cursor._getSiblingData()
		cursor = self.binarySearch(cursor, cursor._firstSiblingLIndex, cursor._lastSiblingLIndex)
		if cursor == None:
			return
		while not cursor.isOut() and self.isOverlapping(cursor) == 0:
			self.write(cursor)
			newCursor = NCListCursor(cursor)
			if newCursor.hasChildren():
				newCursor.moveDown()
				self.compare(newCursor)
			if cursor.isLast():
				return
			cursor.moveRight()
				
	def isOverlapping(self, cursor):
		if self._end < cursor.getStart():
			return 1
		if self._start > cursor.getEnd():
			return -1
		return 0

	def write(self, cursor):
		self._nbOverlaps += 1
		refTranscript = cursor.getTranscript()
		self._overlappingNames.append(refTranscript.getName())

	def dumpWriter(self):
		if (not self._overlappingNames) or self._transcript == None:
			return
		self._transcript.setTagValue("nbOverlaps", len(self._overlappingNames))
		self._transcript.setTagValue("overlapsWith", "--".join(self._overlappingNames))
		self._iWriter.addTranscript(self._transcript)
		self._nbWritten	   += 1
		self._overlappingNames = []

	def run(self):
		self.prepareIntermediateFiles()
		self.createNCList()
		self.compare()
		self.dumpWriter()
		self.close()
		if self._verbosity > 0:
			print "# refs:	%d" % (self._nbLines)
			print "# written: %d (%d overlaps)" % (self._nbOverlappingQueries, self._nbOverlaps)

	
if __name__ == "__main__":
	description = "FindOverlapsWithOneInterval: Finds overlaps with one query interval."

	parser = OptionParser(description = description)
	parser.add_option("-i", "--input",	   dest="inputFileName",	  action="store",			type="string",  help="Input file [compulsory] [format: file in transcript format given by -f]")
	parser.add_option("-f", "--format",	  dest="format",			 action="store",			type="string",  help="Format of previous file [compulsory] [format: transcript file format]")
	parser.add_option("-s", "--start",	   dest="start",			  action="store",			type="int",	 help="The start of the query interval [compulsory] [format: int]")
	parser.add_option("-e", "--end",		 dest="end",				action="store",			type="int",	 help="The end of the query interval [compulsory] [format: int]")
	parser.add_option("-c", "--chromosome",  dest="chromosome",		 action="store",			type="string",  help="Chromosome of the query interval [compulsory] [format: string]")
	parser.add_option("-o", "--output",	  dest="outputFileName",	 action="store",			type="string",  help="Output file [compulsory] [format: output file in GFF3 format]")
	parser.add_option("-v", "--verbosity",   dest="verbosity",		  action="store", default=1, type="int",	 help="Trace level [format: int] [default: 1]")
	(options, args) = parser.parse_args()
	
	iFOWOI = FindOverlapsWithOneInterval(options.verbosity)
	iFOWOI.setFileName(options.inputFileName, options.format)
	iFOWOI.setInterval(options.chromosome, options.start, options.end)
	iFOWOI.setOutputFileName(options.outputFileName)
	iFOWOI.run()