comparison TrackHub.py @ 39:4a69515eed63 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 91271a6c0d39c923f0d460b2979247baa297286b-dirty

38:d17f629f5486

from util import santitizer


class TrackHub:
    def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory, trackType):
        
        self.rootAssemblyHub = None

        self.mySpecieFolderPath = None

        # Store intermediate files, will be removed if not in debug mode
        self.myTracksFolderPath = None

        # Store binary files: Bam, BigWig
        self.myBinaryFolderPath = None

        self.tool_directory = tool_directory

        self.outputFile = outputFile
        self.chromSizesFile = None

        
        # 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()
        
        self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
        #self.cssFolderPath = os.path.join(self.mySpecieFolderPath, 'css')
        #self.cssFilePath = os.path.join(self.cssFolderPath, 'custom_track_styles.css')
        self.logger = logging.getLogger(__name__)

    

    def addTrack(self, trackDbObject):
        if trackDbObject['dataType'].lower() == 'bam':
            #new_track = subprocess.Popen(['echo', trackDbObject['options']], stdout=subprocess.PIPE)
            #subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
            subtools.add_track_json(self.trackList, trackDbObject['options'])
            #subtools.add_track_json(self.trackList, trackDbObject['track_json'])
        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:
            self._removeRaw()
        #self._makeArchive()
        self._outHtml()
        print "Success!\n"


    def _customizeHTMLFeature(self, trackDbObject):

        if not os.path.exists(self.trackList):
            os.mknod(self.trackList)   

    def _prepareRefseq(self):
        subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
        #try:
            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
            #subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference_genome.false_path, '--out', self.mySpecieFolderPath])
        #except OSError as e:
            #print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)

    def _indexName(self):
        #subprocess.call(['generate-names.pl', '-v', '--out', self.mySpecieFolderPath])
        subtools.generate_names(self.mySpecieFolderPath)
        print "finished name index \n"

    def _outHtml(self):
        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
                                  output_encoding='utf-8', encoding_errors='replace')
        htmlTemplate = mylookup.get_template("display.txt")

        with open(self.outputFile, 'w') as htmlfile:
            htmlMakoRendered = htmlTemplate.render(
            species_folder = os.path.relpath(self.mySpecieFolderPath, self.extra_files_path),
            trackList = os.path.relpath(self.trackList, self.extra_files_path)
        )
            htmlfile.write(htmlMakoRendered)
        #with open(self.outputFile, 'w') as htmlfile:
        #    htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name
        #    jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
        #    htmlstr += jbrowse_hub
        #    htmlfile.write(htmlstr)   
          


    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta

        # baseNameFasta = os.path.basename(fasta_file_name)
        # suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
        # nameTwoBit = suffixTwoBit + '.2bit'
        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
        subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)

        # Generate the twoBitInfo
        twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
        subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)

        # Then we get the output to generate the chromSizes
        self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
        subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name) 

        # We can get the biggest scaffold here, with chromSizesFile
        with open(self.chromSizesFile.name, 'r') as chrom_sizes:
            # TODO: Check if exists
            self.default_pos = chrom_sizes.readline().split()[0]

        # TODO: Manage to put every fill Function in a file dedicated for reading reasons
        # Create the root directory
        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

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

        return myHubPath

39:4a69515eed63

from util import santitizer


class TrackHub:
    def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory, trackType):

        self.mySpecieFolderPath = None

        # Store intermediate files, will be removed if not in debug mode
        self.myTracksFolderPath = None

        # Store interval files and their tabix index
        self.myFinalTracksFolderPath = None

        # Store binary files: Bam, BigWig
        self.myBinaryFolderPath = None

        self.tool_directory = tool_directory

        self.outputFile = outputFile
        self.chromSizesFile = None

        
        # Set all the missing variables of this class, and create physically the folders/files
        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()
        if Datatype.trackType == 'HTMLFeatures':
            self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
        self.logger = logging.getLogger(__name__)

    

    def addTrack(self, trackDbObject):
        if trackDbObject['dataType'].lower() == 'bam':
            subtools.add_track_json(self.trackList, trackDbObject['options'])
        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'], trackDbObject['track'], self.myFinalTracksFolderPath)
                subtools.add_track_json(self.trackList, trackDbObject['options'])

    def terminate(self, debug=False):
        """ Write html file """
        self._indexName()
        if not debug:
            self._removeRaw()
        self._outHtml()
        print "Success!\n"


    def _customizeHTMLFeature(self, trackDbObject):

        if not os.path.exists(self.trackList):
            os.mknod(self.trackList)   

    def _prepareRefseq(self):
        subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)

    def _indexName(self):
        subtools.generate_names(self.mySpecieFolderPath)
        print "finished name index \n"

    def _outHtml(self):
        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
                                  output_encoding='utf-8', encoding_errors='replace')
        htmlTemplate = mylookup.get_template("display.txt")

        with open(self.outputFile, 'w') as htmlfile:
            htmlMakoRendered = htmlTemplate.render(
            jbrowse_hub_name = self.reference_genome.assembly_id,
            trackList = os.path.relpath(self.trackList, self.extra_files_path)
        )
            htmlfile.write(htmlMakoRendered)

    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta
        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
        subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)

        # Generate the twoBitInfo
        twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
        subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)

        # Then we get the output to generate the chromSizes
        self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
        subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)

        # We can get the biggest scaffold here, with chromSizesFile
        with open(self.chromSizesFile.name, 'r') as chrom_sizes:
            # TODO: Check if exists
            self.default_pos = chrom_sizes.readline().split()[0]

        # Create the specie folder, use generic name "myHub", to support display JBrowse with Galaxy display application
        mySpecieFolderPath = os.path.join(extra_files_path, "myHub")
        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

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