Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 23:2a12d257f95d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Tue, 14 Mar 2017 16:28:20 -0400
parents fcf2865c950c
children a051609fc8b4
comparison
equal deleted inserted replaced
22:fcf2865c950c 23:2a12d257f95d
57 json_file = os.path.join(self.json, "trackList.json") 57 json_file = os.path.join(self.json, "trackList.json")
58 bam_track = dict() 58 bam_track = dict()
59 bam_track['type'] = 'JBrowse/View/Track/Alignments2' 59 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' 60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
61 bam_track['label'] = track['fileName'] 61 bam_track['label'] = track['fileName']
62 bam_track['urlTemplate'] = os.path.join(self.raw, track['fileName']) 62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
63 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') 63 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
64 print "add bam track\n" 64 print "add bam track\n"
65 elif track['dataType'] == 'bigwig': 65 elif track['dataType'] == 'bigwig':
66 json_file = os.path.join(self.json, "trackList.json") 66 json_file = os.path.join(self.json, "trackList.json")
67 bigwig_track = dict() 67 bigwig_track = dict()
68 bigwig_track['label'] = track['fileName'] 68 bigwig_track['label'] = track['fileName']
69 bigwig_track['urlTemplate'] = os.path.join(self.raw, track['fileName']) 69 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
70 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' 70 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
71 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' 71 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
72 bigwig_track['variance_band'] = True 72 bigwig_track['variance_band'] = True
73 bigwig_track['style'] = dict() 73 bigwig_track['style'] = dict()
74 bigwig_track['style']['pos_color'] = '#FFA600' 74 bigwig_track['style']['pos_color'] = '#FFA600'