comparison TrackHub.py @ 38:d17f629f5486 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty

37:43909f065bee

        # Set all the missing variables of this class, and create physically the folders/files
        self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
        # Init the Datatype 
        Datatype.pre_init(self.reference_genome, self.chromSizesFile,
                          self.extra_files_path, self.tool_directory,
                          self.mySpecieFolderPath, self.myTracksFolderPath, self.myBinaryFolderPath, self.trackType)  

        self._prepareRefseq()
        self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
        self._createTrackList()
        

        elif trackDbObject['dataType'].lower() == 'bigwig':
            subtools.add_track_json(self.trackList, trackDbObject['options'])
        else: 
            if trackDbObject['trackType'] == 'HTMLFeatures':
                self._customizeHTMLFeature(trackDbObject)
            subtools.flatfile_to_json(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['trackType'], trackDbObject['trackLabel'], self.mySpecieFolderPath, trackDbObject['options'])


    def terminate(self, debug=False):
        """ Write html file """
        self._indexName()
        if not debug:

        myHubPath = os.path.join(extra_files_path, "myHub")
        if not os.path.exists(myHubPath):
            os.makedirs(myHubPath)

        # Create the specie folder
        # TODO: Generate the name depending on the specie
        mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
        if not os.path.exists(mySpecieFolderPath):
            os.makedirs(mySpecieFolderPath)
        self.mySpecieFolderPath = mySpecieFolderPath

        # We create the 2bit file while we just created the specie folder
        #self.twoBitName = self.genome_name + ".2bit"
        #self.two_bit_final_path = os.path.join(self.mySpecieFolderPath, self.twoBitName)
        #shutil.copyfile(twoBitFile.name, self.two_bit_final_path)

        # Create the folder tracks into the specie folder
        tracksFolderPath = os.path.join(mySpecieFolderPath, "raw")
        if not os.path.exists(tracksFolderPath):
            os.makedirs(tracksFolderPath)
        self.myTracksFolderPath = tracksFolderPath

        myBinaryFolderPath = os.path.join(mySpecieFolderPath, 'bbi')
        if not os.path.exists(myBinaryFolderPath):
            os.makedirs(myBinaryFolderPath)
        self.myBinaryFolderPath = myBinaryFolderPath

38:d17f629f5486

        # Set all the missing variables of this class, and create physically the folders/files
        self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
        # Init the Datatype 
        Datatype.pre_init(self.reference_genome, self.chromSizesFile,
                          self.extra_files_path, self.tool_directory,
                          self.mySpecieFolderPath, self.myTracksFolderPath, self.myFinalTracksFolderPath, self.myBinaryFolderPath, self.trackType)

        self._prepareRefseq()
        self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
        self._createTrackList()
        

        elif trackDbObject['dataType'].lower() == 'bigwig':
            subtools.add_track_json(self.trackList, trackDbObject['options'])
        else: 
            if trackDbObject['trackType'] == 'HTMLFeatures':
                self._customizeHTMLFeature(trackDbObject)
                subtools.flatfile_to_json(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['trackType'], trackDbObject['trackLabel'], self.mySpecieFolderPath, trackDbObject['options'])
            # Use Tabix index tracks by default for CanvasFeatures
            # TODO: add support for HTMLFeatures
            else:
                subtools.generate_tabix_indexed_track(trackDbObject['trackDataURL'], trackDbObject['dataType'], self.myFinalTracksFolderPath)
                subtools.add_track_json(self.trackList, trackDbObject['options'])

    def terminate(self, debug=False):
        """ Write html file """
        self._indexName()
        if not debug:

        myHubPath = os.path.join(extra_files_path, "myHub")
        if not os.path.exists(myHubPath):
            os.makedirs(myHubPath)

        # Create the specie folder
        mySpecieFolderPath = os.path.join(myHubPath, self.genome_name)
        if not os.path.exists(mySpecieFolderPath):
            os.makedirs(mySpecieFolderPath)
        self.mySpecieFolderPath = mySpecieFolderPath

        # Create the folder named 'raw' inside the specie folder to place raw files
        tracksFolderPath = os.path.join(mySpecieFolderPath, "raw")
        if not os.path.exists(tracksFolderPath):
            os.makedirs(tracksFolderPath)
        self.myTracksFolderPath = tracksFolderPath

        # Create the folder tracks into the specie folder
        finalTracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
        if not os.path.exists(finalTracksFolderPath):
            os.makedirs(finalTracksFolderPath)
        self.myFinalTracksFolderPath = finalTracksFolderPath

        myBinaryFolderPath = os.path.join(mySpecieFolderPath, 'bbi')
        if not os.path.exists(myBinaryFolderPath):
            os.makedirs(myBinaryFolderPath)
        self.myBinaryFolderPath = myBinaryFolderPath