annotate SMART/Java/Python/clusterize.py @ 38:2c0c0a89fad7

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#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
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from commons.core.writer.WriterChooser import WriterChooser
"""Clusterize a set of transcripts"""

import os, os.path, random
from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
from SMART.Java.Python.ncList.FileSorter import FileSorter
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress

class Clusterize(object):

	def __init__(self, verbosity):
		self.normalize		 = False
		self.presorted		 = False
		self.distance		  = 1
		self.colinear		  = False
		self.nbWritten		 = 0
		self.nbMerges		  = 0
		self.verbosity		 = verbosity
		self.splittedFileNames = {}

	def __del__(self):
		for fileName in self.splittedFileNames.values():
			os.remove(fileName)

	def setInputFile(self, fileName, format):
		parserChooser = ParserChooser(self.verbosity)
		parserChooser.findFormat(format)
		self.parser = parserChooser.getParser(fileName)
		self.sortedFileName = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000))
		if "SMARTTMPPATH" in os.environ:
			self.sortedFileName = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileName))

	def setOutputFileName(self, fileName, format="gff3", title="S-MART", feature="transcript", featurePart="exon"):
		writerChooser = WriterChooser()
		writerChooser.findFormat(format)
		self.writer = writerChooser.getWriter(fileName)
		self.writer.setTitle(title)
		self.writer.setFeature(feature)
		self.writer.setFeaturePart(featurePart)

	def setDistance(self, distance):
		self.distance = distance

	def setColinear(self, colinear):
		self.colinear = colinear

	def setNormalize(self, normalize):
		self.normalize = normalize
		
	def setPresorted(self, presorted):
		self.presorted = presorted

	def _sortFile(self):
		if self.presorted:
			return
		fs = FileSorter(self.parser, self.verbosity-4)
		fs.perChromosome(True)
		fs.setPresorted(self.presorted)
		fs.setOutputFileName(self.sortedFileName)
		fs.sort()
		self.splittedFileNames       = fs.getOutputFileNames()
		self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
		self.nbElements              = fs.getNbElements()
		
	def _iterate(self, chromosome):
		if chromosome == None:
			progress = UnlimitedProgress(10000, "Reading input file", self.verbosity)
			parser   = self.parser
		else:
			progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
			parser   = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
		transcripts     = []
		self.nbElements = 0
		for newTranscript in parser.getIterator():
			newTranscripts = []
			if newTranscript.__class__.__name__ == "Mapping":
				newTranscript = newTranscript.getTranscript()
			for oldTranscript in transcripts:
				if self._checkOverlap(newTranscript, oldTranscript):
					self._merge(newTranscript, oldTranscript)
				elif self._checkPassed(newTranscript, oldTranscript):
					self._write(oldTranscript)
				else:
					newTranscripts.append(oldTranscript)
			newTranscripts.append(newTranscript)
			transcripts = newTranscripts
			self.nbElements += 1
			progress.inc()
		for transcript in transcripts:
			self._write(transcript)
		progress.done()

	def _merge(self, transcript1, transcript2):
		self.nbMerges += 1
		transcript2.setDirection(transcript1.getDirection())
		transcript1.merge(transcript2)

	def _write(self, transcript):
		self.nbWritten += 1
		self.writer.addTranscript(transcript)

	def _checkOverlap(self, transcript1, transcript2):
		if transcript1.getChromosome() != transcript2.getChromosome():
			return False
		if self.colinear and transcript1.getDirection() != transcript2.getDirection():
			return False
		if transcript1.getDistance(transcript2) > self.distance:
			return False
		return True

	def _checkPassed(self, transcript1, transcript2):
		return ((transcript1.getChromosome() != transcript2.getChromosome()) or (transcript1.getDistance(transcript2) > self.distance))

	def run(self):
		self._sortFile()
		if self.presorted:
			self._iterate(None)
		else:
			for chromosome in sorted(self.splittedFileNames.keys()):
				self._iterate(chromosome)
		self.writer.close()
		if self.verbosity > 0:
			print "# input:   %d" % (self.nbElements)
			print "# written: %d (%d%% overlaps)" % (self.nbWritten, 0 if (self.nbElements == 0) else ((float(self.nbWritten) / self.nbElements) * 100))
			print "# merges:  %d" % (self.nbMerges)
		

if __name__ == "__main__":
	description = "Clusterize v1.0.3: clusterize the data which overlap. [Category: Merge]"

	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 file [format: transcript file format]")
	parser.add_option("-o", "--output",    dest="outputFileName", action="store",				     type="string", help="output file [compulsory] [format: output file in transcript format given by -u]")
	parser.add_option("-u", "--outputFormat", dest="outputFormat", action="store",     default="gff",		     type="string", help="output file format [format: transcript file format]")
	parser.add_option("-c", "--colinear",  dest="colinear",       action="store_true", default=False,				help="merge colinear transcripts only [format: bool] [default: false]")
	parser.add_option("-d", "--distance",  dest="distance",       action="store",      default=0,     type="int",    help="max. distance between two transcripts to be merged [format: int] [default: 0]")
	parser.add_option("-n", "--normalize", dest="normalize",      action="store_true", default=False,				help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
	parser.add_option("-s", "--sorted",    dest="sorted",		 action="store_true", default=False,				help="input is already sorted [format: bool] [default: false]")
	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()

	c = Clusterize(options.verbosity)
	c.setInputFile(options.inputFileName, options.format)
	c.setOutputFileName(options.outputFileName, options.outputFormat)
	c.setColinear(options.colinear)
	c.setDistance(options.distance)
	c.setNormalize(options.normalize)
	c.setPresorted(options.sorted)
	c.run()