diff trackObject.py @ 39:75edbc203532 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty

--- a/trackObject.py	Fri Mar 17 16:28:21 2017 -0400
+++ b/trackObject.py	Fri Mar 17 19:00:01 2017 -0400
@@ -60,14 +60,22 @@
             utils.gtfToGff3(dataFile, des_path, self.chrom_size)
         track['fileName'] = fileName
         track['dataType'] = dataType
+        self.SetMetadata(track, metaData)
+        self.tracks.append(track)
+
+    #If the metadata is not set, use the default value
+    def SetMetadata(self, track, metaData):
         track.update(metaData)
-        #If the metadata is not set, use the default value
         if 'name' not in metaData.keys() or track['name'] == '':
-            track['name'] = fileName
+            track['name'] = track['fileName']
         if 'label' not in metaData.keys() or track['label'] == '':
             track['label'] = track['name']
         if 'track_color' not in metaData.keys() or track['track_color'] == '':
             track['track_color'] = "#daa520"
         if 'track_type' not in metaData.keys() or track['track_type'] == '':
             track['track_type'] = "CanvasFeatures"
-        self.tracks.append(track)
+        if track['dataType'] == 'bigwig':
+            if 'pos_color' not in metaData.keys() or track['pos_color'] == '':
+                track['pos_color'] = "#FFA600"
+            if 'neg_color' not in metaData.keys() or track['neg_color'] == '':
+                track['neg_color'] = "#005EFF"