Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/ClusterizeByTags.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/ClusterizeByTags.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,157 @@ +#! /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 +from optparse import OptionParser +from commons.core.parsing.ParserChooser import ParserChooser +from commons.core.writer.TranscriptWriter import TranscriptWriter +from SMART.Java.Python.structure.Transcript import Transcript +from SMART.Java.Python.structure.Interval import Interval +from SMART.Java.Python.misc.Progress import Progress +from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection +from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter + + +OPERATIONS = ("diff", "div") +BOOLTOSTRANDS = {True: [0], False: [-1, 1]} + +class ClusterizeByTags(object): + + def __init__(self, verbosity): + self.verbosity = verbosity + self.connection = MySqlConnection(self.verbosity-1) + self.defautValue = None + self.maxDistance = None + self.oneStrand = False + + def setInputFile(self, fileName, format): + chooser = ParserChooser(self.verbosity) + chooser.findFormat(format) + parser = chooser.getParser(fileName) + writer = MySqlTranscriptWriter(self.connection, None, self.verbosity) + writer.addTranscriptList(parser) + writer.write() + self.transcriptTables = writer.getTables() + + def setOutputFile(self, fileName): + self.writer = TranscriptWriter(fileName, "gff3", self.verbosity) + + def setTag(self, tagName, defaultValue): + self.tagName = tagName + self.defaultValue = defaultValue + + def setThreshold(self, threshold): + self.threshold = threshold + + def setOperation(self, operation): + self.operation = operation + if self.operation not in OPERATIONS: + raise Exception("Operation '%s' unsupported: choose among %s" % (self.operation, ", ".join(OPERATIONS))) + + def setMaxDistance(self, distance): + self.maxDistance = distance + + def setOneStrand(self, oneStrand): + self.oneStrand = oneStrand + + def run(self): + for chromosome in sorted(self.transcriptTables.keys()): + progress = Progress(self.transcriptTables[chromosome].getNbElements(), "Analyzing %s" % (chromosome), self.verbosity) + for strand in BOOLTOSTRANDS[self.oneStrand]: + previousValue = None + previousTrend = None + previousTranscript = None + sumValue = 0 + command = "SELECT * FROM %s" % (self.transcriptTables[chromosome].getName()) + if not self.oneStrand: + command += " WHERE direction = %d" % (strand) + command += " ORDER BY start, end" + for index, transcript in self.transcriptTables[chromosome].selectTranscripts(command): + if self.tagName in transcript.getTagNames(): + value = transcript.getTagValue(self.tagName) + else: + value = self.defaultValue + if previousValue == None: + trend = None + else: + if self.operation == "diff": + trend = value - previousValue + else: + trend = value / previousValue + if previousTranscript == None: + sumValue = value + elif (previousTrend == None or abs(trend - previousTrend) <= self.threshold) and (self.maxDistance == None or previousTranscript.getDistance(transcript) <= self.maxDistance) and (previousTranscript.getDirection() == transcript.getDirection() or not self.oneStrand): + if previousTranscript.getDirection() != transcript.getDirection(): + transcript.reverse() + previousTranscript.merge(transcript) + transcript = previousTranscript + sumValue += value + previousTrend = trend + else: + previousTranscript.setTagValue(self.tagName, sumValue) + self.writer.addTranscript(previousTranscript) + sumValue = value + previousTrend = None + previousValue = value + previousTranscript = transcript + progress.inc() + if previousTranscript != None: + previousTranscript.setTagValue(self.tagName, sumValue) + self.writer.addTranscript(previousTranscript) + progress.done() + self.writer.close() + + +if __name__ == "__main__": + + description = "Clusterize By Tags v1.0.1: Clusterize a set of element using their tag values. [Category: Merge]" + + parser = OptionParser(description = description) + parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="query 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("-t", "--tag", dest="tagName", action="store", type="string", help="name of the tag [format: string] [compulsory]") + parser.add_option("-e", "--default", dest="defaultValue", action="store", default=None, type="int", help="default value for the tag [format: string]") + parser.add_option("-r", "--threshold", dest="threshold", action="store", type="int", help="threshold between two consecutive tags [format: int] [compulsory]") + parser.add_option("-p", "--operation", dest="operation", action="store", type="string", help="operation to apply between 2 different clusters to compare them [format: choice (diff, div)] [compulsory]") + parser.add_option("-d", "--distance", dest="maxDistance", action="store", default=None, type="int", help="maximum distance for 2 clusters to be merged [format: int] [default: None]") + parser.add_option("-1", "--oneStrand", dest="oneStrand", action="store_true", default=False, help="also cluster the elements which are on different strands [format: bool] [default: False]") + 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() + + cbt = ClusterizeByTags(options.verbosity) + cbt.setInputFile(options.inputFileName, options.format) + cbt.setOutputFile(options.outputFileName) + cbt.setTag(option.tagName, option.defaultValue) + cbt.setThreshold(option.threshold) + cbt.setOperation(option.operation) + cbt.setMaxDistance(operation.maxDistance) + cbt.setOneStrand(operation.oneStrand) + cbt.run()