diff tracks/BamFeatures.py @ 25:31a41ce128cc draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tracks/BamFeatures.py	Fri Oct 13 12:44:31 2017 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+import os
+import json
+import logging
+
+from TrackDb import TrackDb
+from util import subtools
+from util import santitizer
+
+
+class BamFeatures(TrackDb):
+    def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
+        super(BamFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
+ 
+    def prepareExtraSetting(self):
+        if 'category' not in self.extraSettings or not self.extraSettings['category']:
+            self.extraSettings['category'] = "Default group"
+        bam_track = dict()
+        bam_track['type'] = 'JBrowse/View/Track/Alignments2'
+        bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
+        bam_track['urlTemplate'] = os.path.join('bbi', self.trackName)
+        bam_track['baiUrlTemplate'] = os.path.join('bbi', self.extraSettings['index'])
+        bam_track['label'] = self.trackLabel
+        bam_track['category'] = self.extraSettings['category']
+        #extraConfigs = json.dumps(bam_track)
+        extraConfigs = bam_track
+        return extraConfigs
+
+    
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