Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsBin.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervalsBin.py Tue Apr 30 15:02:29 2013 -0400 @@ -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() +