diff TrackHub.py @ 24:bb6fdccef474 draft

Uploaded

--- a/TrackHub.py	Fri Jul 07 17:08:32 2017 -0400
+++ b/TrackHub.py	Wed Jul 12 12:55:27 2017 -0400
@@ -56,7 +56,11 @@
             self.Bam(track, metadata)
            # print "add bam track\n"
         elif track['dataType'] == 'bigwig':
-            self.BigWig(track, metadata)
+            #create trackList.json if not exist
+            self.createTrackList()
+            json_file = os.path.join(self.json, "trackList.json")
+            bigwig_file = os.path.join(self.raw, track['fileName'])
+            subprocess.call(['add-bw-track.pl', '--label', metadata['label'], '--bw_url', bigwig_file, '--pos_color', metadata['style']['pos_color'], '--neg_color', metadata['style']['neg_color'], '--plot', 'JBrowse/View/Track/Wiggle/XYPlot', '--out', json_file, '--in', json_file])
         else: 
             flat_file = os.path.join(self.raw, track['fileName'])
             if track['dataType'] == 'bed':
@@ -118,7 +122,7 @@
         #Use add-track-json.pl to add bam track to json file
         new_track = subprocess.Popen(['echo', bam_track], stdout=subprocess.PIPE)
         subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
-    
+    '''
     def BigWig(self, track, metadata):
         #create trackList.json if not exist
         self.createTrackList()
@@ -135,7 +139,8 @@
         new_track = subprocess.Popen(['echo', bigwig_track], stdout=subprocess.PIPE)
         #output = new_track.communicate()[0]
         subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
-
+    '''
+    def BigWig
     #If the metadata is not set, use the default value
     def SetMetadata(self, track, metadata):
         if 'label' not in metadata.keys() or metadata['label'] == '':