annotate SMART/Java/Python/structure/TranscriptList.py @ 62:8c42a6d7ffd4

Added simple test BED file.

#
# Copyright INRA-URGI 2009-2010
# 
# 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".
# 
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# 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,
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# 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
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# The fact that you are presently reading this means that you have had
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from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.mySql.MySqlTable import MySqlTable
from SMART.Java.Python.structure.Interval import Interval
from SMART.Java.Python.misc.Progress import Progress


class TranscriptList(object):
    """A class that codes for a list of transcript"""

    def __init__(self, verbosity = 0):
        self.transcripts = dict()
        self.longestTranscript = 0
        self.verbosity = verbosity


    def getTranscript(self, chromosome, index):
        return self.transcripts[chromosome][index]
        

    def getChromosomes(self):
        return self.transcripts.keys()


    def getTranscriptsOnChromosome(self, chromosome):
        if chromosome not in self.transcripts:
            return []
        return self.transcripts[chromosome]


    def addTranscript(self, transcript):
        if transcript.getChromosome() in self.transcripts:
            self.transcripts[transcript.getChromosome()].append(transcript)
        else:
            self.transcripts[transcript.getChromosome()] = [transcript]
        self.longestTranscript = max(self.longestTranscript, transcript.getEnd() - transcript.getStart())
        

    def removeTranscript(self, chromosome, i):
        del self.transcripts[chromosome][i]


    def removeAll(self):
        self.transcripts = {}


    def getNbTranscripts(self):
        nbTranscripts = 0
        for chromosome in self.transcripts:
            nbTranscripts += len(self.transcripts[chromosome])
        return nbTranscripts


    def getSize(self):
        size = 0
        for chromosome in self.transcripts:
            for transcript in self.transcripts[chromosome]:
                size += transcript.getSize()
        return size


    def sort(self):
        for chromosome in self.transcripts:
            self.transcripts[chromosome].sort(lambda x, y: x.getStart() - y.getStart())


    def removeOverlapWith(self, transcriptList):
        transcriptList.sort()
        for chromosome in self.transcripts:
            progress = Progress(len(self.transcripts[chromosome]), "Handling chromosome %s" % (chromosome), self.verbosity)
            for thisTranscriptId in range(len(self.transcripts[chromosome])):
                progress.inc()
                for thatTranscriptId in range(len(transcriptList.transcripts[chromosome])):
                    if self.transcripts[chromosome][thisTranscriptId].overlapWith(transcriptList.transcripts[chromosome][thatTranscriptId]):
                        self.transcripts[chromosome][thisTranscriptId] = None
                        break
                    if self.transcripts[chromosome][thisTranscriptId].getEnd() > transcriptList.transcripts[chromosome][thatTranscriptId]:
                        break
            self.transcripts[chromosome] = [transcript for transcript in self.transcripts[chromosome] if transcript != None]
        progress.done()


    def removeOverlapWithExon(self, transcriptList):
        transcriptList.sort()
        for chromosome in self.transcripts:
            progress = Progress(len(self.transcripts[chromosome]), "Handling chromosome %s" % (chromosome), self.verbosity)
            for thisTranscriptId in range(len(self.transcripts[chromosome])):
                progress.inc()
                for thatTranscriptId in range(len(transcriptList.transcripts[chromosome])):
                    if self.transcripts[chromosome][thisTranscriptId].overlapWithExon(transcriptList.transcripts[chromosome][thatTranscriptId]):
                        self.transcripts[chromosome][thisTranscriptId] = None
                        break
                    if self.transcripts[chromosome][thisTranscriptId].getEnd() > transcriptList.transcripts[chromosome][thatTranscriptId]:
                        break
            self.transcripts[chromosome] = [transcript for transcript in self.transcripts[chromosome] if transcript != None]
        progress.done()


    def setDefaultTagValue(self, name, value):
        for transcript in self.getIterator():
            transcript.setTag(name, value)


    def storeDatabase(self, mySqlConnection):
        transcriptsTable = MySqlTable("TmpTranscriptsTable", mySqlConnection)
        transcriptsTable.create(Transcript.getSqlVariables(), Transcript.getSqlTypes())
        intervalsVariables = Interval.getSqlVariables()
        intervalsVariables.append("idTranscript")
        intervalsTypes = Interval.getSqlTypes()
        intervalsTypes["idTranscript"] = "int"
        intervalsTable = MySqlTable("TmpIntervalsTable", mySqlConnection)
        intervalsTable.create(intervalsVariables, intervalsTypes)
        for chromosome in self.transcripts:
            for transcript in self.transcripts[chromosome]:
                idTranscript = transcriptsTable.addLine(transcript.getSqlValues())
                for exon in transcript.getExons():
                    intervalValues = exon.getSqlValues()
                    intervalValues["idTranscript"] = idTranscript
                    intervalsTable.addLine(intervalValues)
                    
    
    def getIterator(self):
        chromosomes = self.transcripts.keys()
        currentChromosome = 0
        currentTranscript = 0
        while True:
            if currentChromosome >= len(chromosomes):
                return
            elif currentTranscript >= len(self.transcripts[chromosomes[currentChromosome]]):
                currentTranscript    = 0
                currentChromosome += 1
            elif self.transcripts[chromosomes[currentChromosome]][currentTranscript] == None:
                currentTranscript += 1
            else:
                yield self.transcripts[chromosomes[currentChromosome]][currentTranscript]
                currentTranscript += 1


    def __str__(self):
        string = ""
        for transcript in self.getIterator():
            string += str(transcript)
        return string