--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Gff3.py	Wed Dec 21 12:13:04 2016 -0500
@@ -0,0 +1,67 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+# Internal dependencies
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class Gff3( Datatype ):
+    def __init__(self, input_Gff3_false_path, data_gff3):
+        super( Gff3, self ).__init__()
+
+        self.track = None
+
+        self.input_Gff3_false_path = input_Gff3_false_path
+        self.name_gff3 = data_gff3["name"]
+        self.priority = data_gff3["order_index"]
+        self.track_color = data_gff3["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_gff3["group_name"]
+
+        # TODO: See if we need these temporary files as part of the generated files
+        unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
+        unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
+        sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
+
+        # gff3ToGenePred processing
+        subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
+
+        # genePredToBigGenePred
+        subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
+
+        # Sort processing
+        subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
+
+        # TODO: Check if no errors
+
+        # bedToBigBed processing
+        trackName = "".join( (self.name_gff3, ".bb" ) )
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sorted_biGenePred_file.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+8',
+                                 tab=True)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_gff3,
+                         track_type='bigGenePred', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        print("- Gff3 %s created" % self.name_gff3)