--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSpliceJunctions.py	Fri Jan 20 17:12:03 2017 -0500
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class BedSpliceJunctions( Datatype ):
+    def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions):
+
+        super(BedSpliceJunctions, self).__init__()
+
+        self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path
+        self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
+        self.priority = data_bed_splice_junctions["order_index"]
+        self.track_color = data_bed_splice_junctions["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bed_splice_junctions["group_name"]
+
+        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+
+        # Sort processing
+        subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + .bb
+        trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) )
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as')
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed12+1',
+                                 autoSql=auto_sql_option)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_bed_simple_repeats,
+        #     shortLabel=self.getShortName( self.name_bed_simple_repeats ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed 4 +',
+        #     visibility='dense',
+        #     priority=self.priority,
+        # )
+        #
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bed splice junctions %s created" % self.name_bed_splice_junctions)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))