diff datatypes/Datatype.py @ 83:0bc486356e2a draft

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

--- a/datatypes/Datatype.py	Wed Sep 27 17:31:19 2017 -0400
+++ b/datatypes/Datatype.py	Mon Oct 30 12:01:23 2017 -0400
@@ -96,110 +96,3 @@
     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"        
-    '''
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