diff TrackHub.py @ 37:046c5bfc0413 draft

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

--- a/TrackHub.py	Fri Mar 17 13:04:11 2017 -0400
+++ b/TrackHub.py	Fri Mar 17 16:21:25 2017 -0400
@@ -44,37 +44,43 @@
             print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
     #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
     def addTrack(self, track):
+        track_label = track['label']
+        track_color = track['track_color']
+        track_type = track['track_type']
         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['label']
+            bam_track['label'] = track_label
+            bam_track['color'] = track_color
             bam_track['urlTemplate'] = 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"
+           # 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['label']
+            bigwig_track['label'] = track_label
+            bigwig_track['color'] = track_color
             bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
             bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
             bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
             utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
         else: 
             gff3_file = os.path.join(self.raw, track['fileName'])
-            label = track['label']
             if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':
-                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json])
+                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "color" : "%s"}' % track_color, '--out', self.json])
             elif track['dataType'] == 'gff3_transcript':
-                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--config', '{"transcriptType": "transcript"}', '--out', self.json])
+                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"transcriptType": "transcript", "color" : "%s"}' % track_color, '--out', self.json])
             elif track['dataType'] == 'gff3_mrna':
-                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--out', self.json])
+                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json])
+            elif track['dataType'] == 'blastxml':
+                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json])
             else:
-                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', self.json])
+                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--config', '{"color" : "%s"}' % track_color, '--out', self.json])
             p.communicate()
             
     def indexName(self):