--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSimpleRepeats.py	Wed Jul 13 13:36:37 2016 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class BedSimpleRepeats( Datatype ):
+    def __init__( self, input_bed_simple_repeats_false_path, data_bed_simple_repeats,
+                 input_fasta_file, extra_files_path, tool_directory ):
+
+        super(BedSimpleRepeats, self).__init__(
+                input_fasta_file, extra_files_path, tool_directory
+        )
+
+        self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
+        self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
+        self.priority = data_bed_simple_repeats["order_index"]
+
+        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+        twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
+        chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
+
+        # Sort processing
+        subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
+
+        # TODO: Regroup in an mother class which handles the Chrom.sizes creation with Gff3 and Gtf
+        # Generate the chrom.sizes
+
+        subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name)
+
+        # Then we get the output to inject into the sort
+        # TODO: Check if no errors
+        subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + .bb
+        trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+        auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name,
+                                 typeOption='-type=bed4+12',
+                                 autoSql=auto_sql_option)
+
+        # Create the Track Object
+        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("- %s created in %s" % (trackName, myBigBedFilePath))