Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 22:fcf2865c950c 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 16:23:09 -0400
parents 7e1c25080972
children 2a12d257f95d
comparison
equal deleted inserted replaced
21:7e1c25080972 22:fcf2865c950c
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['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
60 bam_track['label'] = track['fileName'] 61 bam_track['label'] = track['fileName']
61 bam_track['urlTemplate'] = os.path.join(self.raw, track['fileName']) 62 bam_track['urlTemplate'] = os.path.join(self.raw, track['fileName'])
62 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') 63 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
63 print "add bam track\n" 64 print "add bam track\n"
64 elif track['dataType'] == 'bigwig': 65 elif track['dataType'] == 'bigwig':
65 json_file = os.path.join(self.json, "trackList.json") 66 json_file = os.path.join(self.json, "trackList.json")
66 bigwig_track = dict() 67 bigwig_track = dict()
67 bigwig_track['label'] = track['fileName'] 68 bigwig_track['label'] = track['fileName']
68 bigwig_track['urlTemplate'] = os.path.join(self.raw, track['fileName']) 69 bigwig_track['urlTemplate'] = os.path.join(self.raw, track['fileName'])
69 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'
70 bigwig_track['variance_band'] = True 72 bigwig_track['variance_band'] = True
71 bigwig_track['style'] = dict() 73 bigwig_track['style'] = dict()
72 bigwig_track['style']['pos_color'] = '#FFA600' 74 bigwig_track['style']['pos_color'] = '#FFA600'
73 bigwig_track['style']['neg_color'] = '#005EFF' 75 bigwig_track['style']['neg_color'] = '#005EFF'
74 bigwig_track['style']['clip_marker_color'] = 'red' 76 bigwig_track['style']['clip_marker_color'] = 'red'