annotate SMART/Java/Python/ClusterizeByTags.py @ 6:769e306b7933

Change the repository level.

#! /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()