--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bed.py	Wed Jul 13 13:36:37 2016 -0400
@@ -0,0 +1,72 @@
+#!/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 Bed( Datatype ):
+    def __init__( self, inputBedGeneric, data_bed_generic,
+                 inputFastaFile, extra_files_path, tool_directory ):
+        super(Bed, self).__init__(
+            inputFastaFile, extra_files_path, tool_directory
+        )
+
+        self.track = None
+
+        self.inputBedGeneric = inputBedGeneric
+
+        self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+        self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
+        self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
+
+        self.data_bed_generic = data_bed_generic
+        self.name_bed_generic = self.data_bed_generic["name"]
+        self.priority = self.data_bed_generic["order_index"]
+
+        # Sort processing
+        subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
+
+        # Generate the chrom.sizes
+        # TODO: Isolate in a function
+        # We first get the twoBit Infos
+        subtools.twoBitInfo(self.twoBitFile.name, self.twoBitInfoFile.name)
+
+        # Then we get the output to inject into the sort
+        # TODO: Check if no errors
+        subtools.sortChromSizes(self.twoBitInfoFile.name, self.chromSizesFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
+        trackName = "".join( ( self.name_bed_generic, ".bb") )
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+        with open(myBigBedFilePath, 'w') as self.bigBedFile:
+            subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
+
+        # Create the Track Object
+        dataURL = "tracks/%s" % trackName
+
+        trackDb = TrackDb(
+            trackName=trackName,
+            longLabel=self.name_bed_generic,
+            shortLabel=self.getShortName(self.name_bed_generic),
+            trackDataURL=dataURL,
+            trackType='bigBed',
+            visibility='dense',
+            thickDrawItem='on',
+            priority=self.priority,
+        )
+
+        # Return the BigBed track
+        self.track = Track(
+            trackFile=myBigBedFilePath,
+            trackDb=trackDb,
+        )
+
+        print("- %s created in %s" % (trackName, myBigBedFilePath))