comparison datatypes/Datatype.py @ 3:fa990284327b draft default tip

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty

2:7486909dfc22

        """Create the final track file"""

    def createTrackDb(self):
        self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)

    
   

        
    
        
    '''
    def __init__(self):
        not_init_message = "The {0} is not initialized." \
                           "Did you use pre_init static method first?"
        if Datatype.input_fasta_file is None:
            raise TypeError(not_init_message.format('reference genome'))
        if Datatype.extra_files_path is None:
            raise TypeError(not_init_message.format('track Hub path'))
        if Datatype.tool_directory is None:
            raise TypeError(not_init_message.format('tool directory'))
        self.track = None
        self.extra_settings = collections.OrderedDict()
        

    @staticmethod
    def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
                 extra_files_path, tool_directory, specie_folder, tracks_folder):
        Datatype.extra_files_path = extra_files_path
        Datatype.tool_directory = tool_directory

        # TODO: All this should be in TrackHub and not in Datatype
        Datatype.mySpecieFolderPath = specie_folder
        Datatype.myTrackFolderPath = tracks_folder

        Datatype.input_fasta_file = reference_genome

        # 2bit file creation from input fasta
        Datatype.twoBitFile = two_bit_path
        Datatype.chromSizesFile = chrom_sizes_file
 
    @staticmethod
    def get_largest_scaffold_name(self):
        # We can get the biggest scaffold here, with chromSizesFile
        with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
            # TODO: Check if exists
            return chrom_sizes.readline().split()[0]
  

    def createTrack(self, trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings=None):
        self.track = TrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings)

    def initRequiredSettings(self, trackSettings, trackDataURL = None, trackType = None):
        
        #Initialize required fields: trackName, longLabel, shortLable
      
        self.trackSettings = trackSettings
        self.trackName = self.trackSettings["name"]
        #self.priority = self.trackSettings["order_index"]
        #self.track_color = self.trackSettings["track_color"]
        # TODO: Think about how to avoid repetition of the group_name everywhere
        #self.group_name = self.trackSettings["group_name"]
        #self.database = self.trackSettings["database"]
        if self.trackSettings["long_label"]:
            self.longLabel = self.trackSettings["long_label"]
        else:
            self.longLabel = self.trackName
        if not "short_label" in self.trackSettings:
            self.shortLabel = ""
        else:
            self.shortLabel = self.trackSettings["short_label"]
        self.trackDataURL = trackDataURL
        self.trackType = trackType
    
    def setExtLink(self, database, inputFile, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
        if "NCBI" in database:
            if not seqType:
                self.seqType = int(self.getSeqType(inputFile))
            else:
                self.seqType = seqType
            if self.seqType < 0:
                print self.seqType
                raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
            if self.seqType == 2:
                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
            elif self.seqType == 1:
                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
            else:
                raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(self.seqType))
        elif "UniProt" in database:
            self.extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
        elif "FlyBase" in database:
            self.extra_settings["url"] = "http://flybase.org/reports/$$"
        else:
            self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
        self.extra_settings["urlLabel"] = database + " Details:"
        if useIframe:
            self.extra_settings["iframeUrl"] = self.extra_settings["url"]
            if not iframeHeight:
                iframeHeight = "600"
            if not iframeWidth:
                iframeWidth = "800"
            self.extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)

    def getSeqType(self, inputFile):
        with open(inputFile, "r") as bigpsl:
            sampleSeq = bigpsl.readline().split()
        if len(sampleSeq) == 25:
            return sampleSeq[-1]
        else:
            return "-1"        
    '''

3:fa990284327b

        """Create the final track file"""

    def createTrackDb(self):
        self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)