Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 20:49841ae99869 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 15:37:10 -0400
parents 8627394693c6
children 7e1c25080972
comparison
equal deleted inserted replaced
19:2edc47a6d575 20:49841ae99869
55 def addTrack(self, track): 55 def addTrack(self, track):
56 if track['dataType'] == 'bam': 56 if track['dataType'] == 'bam':
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['label'] = track.fileName 60 bam_track['label'] = track['fileName']
61 bam_track['urlTemplate'] = os.path.join('../raw', track.fileName) 61 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
62 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') 62 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
63 print "add bam track\n" 63 print "add bam track\n"
64 elif track['dataType'] == 'bigwig': 64 elif track['dataType'] == 'bigwig':
65 json_file = os.path.join(self.json, "trackList.json") 65 json_file = os.path.join(self.json, "trackList.json")
66 bigwig_track = dict() 66 bigwig_track = dict()
67 bigwig_track['label'] = 'rnaseq' 67 bigwig_track['label'] = 'rnaseq'
68 bigwig_track['key'] = 'RNA-Seq Coverage' 68 bigwig_track['key'] = 'RNA-Seq Coverage'
69 bigwig_track['urlTemplate'] = os.path.join('../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['variance_band'] = True 71 bigwig_track['variance_band'] = True
72 bigwig_track['style'] = dict() 72 bigwig_track['style'] = dict()
73 bigwig_track['style']['pos_color'] = '#FFA600' 73 bigwig_track['style']['pos_color'] = '#FFA600'
74 bigwig_track['style']['neg_color'] = '#005EFF' 74 bigwig_track['style']['neg_color'] = '#005EFF'