diff SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsBin.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsBin.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,204 @@
+#! /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.
+#
+import random, os, os.path, time, sqlite3
+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
+try:
+   import cPickle as pickle
+except:
+   import pickle
+
+MINBIN = 3
+MAXBIN = 7
+
+
+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 FindOverlapsWithSeveralIntervalsBin(object):
+
+	def __init__(self, verbosity):
+		self.verbosity	= verbosity
+		self.randomNumber = random.randint(0, 10000)
+		self.dbName	   = "smartdb%d" % (self.randomNumber)
+		if "SMARTTMPPATH" in os.environ:
+			self.dbName = os.join(os.environ["SMARTTMPPATH"], self.dbName)
+		self.connection = sqlite3.connect(self.dbName)
+		self.tableNames = {}
+		self.nbQueries  = 0
+		self.nbRefs	 = 0
+		self.nbWritten  = 0
+		self.nbOverlaps = 0
+		cursor = self.connection.cursor()
+		cursor.execute("PRAGMA journal_mode = OFF")
+		cursor.execute("PRAGMA synchronous = 0")
+		cursor.execute("PRAGMA locking_mode = EXCLUSIVE")
+		cursor.execute("PRAGMA count_change = OFF")
+		cursor.execute("PRAGMA temp_store = 2")
+
+	def __del__(self):
+		cursor = self.connection.cursor()
+		for tableName in self.tableNames.values():
+			cursor.execute("DROP TABLE IF EXISTS %s" % (tableName))
+		if os.path.exists(self.dbName):
+			os.remove(self.dbName)
+		
+	def createTable(self, chromosome):
+		cursor = self.connection.cursor()
+		tableName = "tmpTable_%s_%d" % (chromosome.replace("-", "_"), self.randomNumber)
+		cursor.execute("CREATE TABLE %s (start INT, end INT, transcript BLOB, bin INT)" % (tableName))
+		cursor.execute("CREATE INDEX index_%s ON %s (bin)" % (tableName, tableName))
+		self.tableNames[chromosome] = tableName
+
+	def setReferenceFile(self, fileName, format):
+		chooser = ParserChooser(self.verbosity)
+		chooser.findFormat(format)
+		parser = chooser.getParser(fileName)
+		startTime = time.time()
+		if self.verbosity > 2:
+			print "Storing into table"
+		for transcript in parser.getIterator():
+			if transcript.__class__.__name__ == "Mapping":
+				transcript = transcript.getTranscript()
+			transcriptString = pickle.dumps(transcript)
+			chromosome = transcript.getChromosome()
+			if chromosome not in self.tableNames:
+				self.createTable(chromosome)
+			start	  = transcript.getStart()
+			end		= transcript.getEnd()
+			bin		= getBin(start, end)
+			cursor	 = self.connection.cursor()
+			cursor.execute("INSERT INTO %s (start, end, transcript, bin) VALUES (?, ?, ?, ?)" % (self.tableNames[chromosome]), (start, end, sqlite3.Binary(transcriptString), bin))
+			self.nbRefs += 1
+		self.connection.commit()
+		endTime = time.time()
+		if self.verbosity > 2:
+			print "	...done (%.2gs)" % (endTime - startTime)
+
+	def setQueryFile(self, fileName, format):
+		chooser = ParserChooser(self.verbosity)
+		chooser.findFormat(format)
+		self.queryParser = chooser.getParser(fileName)
+		self.nbQueries = self.queryParser.getNbItems()
+
+	def setOutputFile(self, fileName):
+		self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+
+	def compare(self):
+		progress = Progress(self.nbQueries, "Reading queries", self.verbosity)
+		startTime = time.time()
+		for queryTranscript in self.queryParser.getIterator():
+			if queryTranscript.__class__.__name__ == "Mapping":
+				queryTranscript = queryTranscript.getTranscript()
+			progress.inc()
+			queryChromosome = queryTranscript.getChromosome()
+			if queryChromosome not in self.tableNames:
+				continue
+			queryStart = queryTranscript.getStart()
+			queryEnd   = queryTranscript.getEnd()
+			bins	   = getOverlappingBins(queryStart, queryEnd)
+			commands   = []
+			for bin in bins:
+				command = "SELECT * FROM %s WHERE bin " % (self.tableNames[queryChromosome])
+				if bin[0] == bin[1]:
+					command += "= %d" % (bin[0])
+				else:
+					command += "BETWEEN %d AND %d" % (bin[0], bin[1])
+				commands.append(command)
+			command = " UNION ".join(commands)
+			cursor  = self.connection.cursor()
+			cursor.execute(command)
+			overlap = False
+			line	= cursor.fetchone()
+			while line:
+				refStart, refEnd, refTranscriptString, refBin = line
+				if refStart <= queryEnd and refEnd >= queryStart:
+					refTranscript = pickle.loads(str(refTranscriptString))
+					if refTranscript.overlapWith(queryTranscript):
+						overlap = True
+						self.nbOverlaps += 1
+				line = cursor.fetchone()
+			if overlap:
+				self.writer.addTranscript(queryTranscript)
+				self.nbWritten += 1
+		progress.done()
+		endTime = time.time()
+		self.timeSpent = endTime - startTime
+
+	def displayResults(self):
+		print "# queries:  %d" % (self.nbQueries)
+		print "# refs:	   %d" % (self.nbRefs)
+		print "# written:  %d (%d overlaps)" % (self.nbWritten, self.nbOverlaps)
+		print "time:	   %.2gs" % (self.timeSpent)
+
+	def run(self):
+		self.compare()
+		self.displayResults()
+
+if __name__ == "__main__":
+	
+	description = "Find Overlaps With Several Intervals Using Bin v1.0.1: Use MySQL binning to compare intervals. [Category: Personal]"
+
+	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()
+
+	fowsib = FindOverlapsWithSeveralIntervalsBin(options.verbosity)
+	fowsib.setQueryFile(options.inputFileName1, options.format1)
+	fowsib.setReferenceFile(options.inputFileName2, options.format2)
+	fowsib.setOutputFile(options.outputFileName)
+	fowsib.run()
+