diff Gtf.py @ 11:d05236b15f81 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2

--- a/Gtf.py	Thu Jul 21 05:58:51 2016 -0400
+++ b/Gtf.py	Wed Jul 27 10:10:49 2016 -0400
@@ -21,7 +21,7 @@
         self.name_gtf = data_gtf["name"]
         self.priority = data_gtf["order_index"]
 
-        print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
+        #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
 
         # TODO: See if we need these temporary files as part of the generated files
         genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
@@ -46,20 +46,26 @@
             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_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
+                         track_file=myBigBedFilePath)
+        #
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_gtf,
+        #     shortLabel=self.getShortName( self.name_gtf ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed 12 +',
+        #     visibility='dense',
+        #     priority=self.priority,
+        # )
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
 
-        trackDb = TrackDb(
-            trackName=trackName,
-            longLabel=self.name_gtf,
-            shortLabel=self.getShortName( self.name_gtf ),
-            trackDataURL=dataURL,
-            trackType='bigBed 12 +',
-            visibility='dense',
-            priority=self.priority,
-        )
-        self.track = Track(
-            trackFile=myBigBedFilePath,
-            trackDb=trackDb,
-        )
-
-        print("- %s created in %s" % (trackName, myBigBedFilePath))
+        print("- Gtf %s created" % self.name_gtf)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))