diff TrackHub.py @ 26:a4a54b925c73 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

--- a/TrackHub.py	Tue Mar 14 17:41:29 2017 -0400
+++ b/TrackHub.py	Wed Mar 15 10:51:23 2017 -0400
@@ -54,16 +54,18 @@
     #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
     def addTrack(self, track):
         if track['dataType'] == 'bam':
+            self.createTrackList()
             json_file = os.path.join(self.json, "trackList.json")
             bam_track = dict()
             bam_track['type'] = 'JBrowse/View/Track/Alignments2'
             bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
             bam_track['label'] = track['fileName']
             bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
-            #bam_track['baiUrlTemplate'] = os.path.join('../raw', track['fileName'])
+            bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
             utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
             print "add bam track\n"
         elif track['dataType'] == 'bigwig':
+            self.createTrackList()
             json_file = os.path.join(self.json, "trackList.json")
             bigwig_track = dict()
             bigwig_track['label'] = track['fileName']
@@ -113,6 +115,13 @@
             #htmlstr = htmlstr % zipfile
             htmlfile.write(htmlstr)
 
+    def createTrackList(self):
+        trackList = os.path.join(self.json, "trackList.json")
+        if not os.path.exists(trackList):
+            os.mknod(trackList)
+            #open(trackList,'w').close()
+            
+