diff Gff3.py @ 11:d05236b15f81 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author rmarenco
date Wed, 27 Jul 2016 10:10:49 -0400
parents acc233161f50
children 25809f699cb3
line wrap: on
line diff
--- a/Gff3.py	Thu Jul 21 05:58:51 2016 -0400
+++ b/Gff3.py	Wed Jul 27 10:10:49 2016 -0400
@@ -47,21 +47,27 @@
             subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
 
         # Create the Track Object
-        dataURL = "tracks/%s" % trackName
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_gff3, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
+                         track_file=myBigBedFilePath)
 
-        trackDb = TrackDb(
-            trackName=trackName,
-            longLabel=self.name_gff3,
-            shortLabel=self.getShortName( self.name_gff3 ),
-            trackDataURL=dataURL,
-            trackType='bigBed 12 +',
-            visibility='dense',
-            priority=self.priority,
-        )
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_gff3,
+        #     shortLabel=self.getShortName( self.name_gff3 ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed 12 +',
+        #     visibility='dense',
+        #     priority=self.priority,
+        # )
+        #
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
 
-        self.track = Track(
-            trackFile=myBigBedFilePath,
-            trackDb=trackDb,
-        )
-
-        print("- %s created in %s" % (trackName, myBigBedFilePath))
+        print("- Gff3 %s created" % self.name_gff3)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))